8U0R | pdb_00008u0r

The crystal structure of protein A21, a component of the conserved poxvirus entry-fusion complex

PDB DOI: https://doi.org/10.2210/pdb8U0R/pdb

Classification: VIRAL PROTEIN
Organism(s): Vaccinia virus Western Reserve
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-29 Released: 2024-09-04
Deposition Author(s): Diesterbeck, U., Gittis, A.G., Garboczi, D.N., Moss, B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.239 (Depositor), 0.243 (DCC)
R-Value Work:
0.211 (Depositor), 0.217 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The 2.3 angstrom Structure of A21, a Protein Component of the Conserved Poxvirus Entry-Fusion Complex.

Diesterbeck, U.S., Muslinkina, L.A., Gittis, A.G., Singh, K., Moss, B., Garboczi, D.N.

(2025) J Mol Biology 437: 169097-169097

PubMed: 40118206 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2025.169097
Primary Citation of Related Structures:
8U0R

PubMed Abstract:
Poxviruses are exceptional in having an entry-fusion complex (EFC) consisting of eleven conserved proteins embedded in the membrane of mature virions. With the goal of understanding the function of the EFC, extensive efforts have been made to determine the structures and roles of its components, and to date, structures have been determined for nine of the eleven proteins. Here, we report the crystal structure of A21, the 10th EFC protein, comprising two α-helices clasping a twisted antiparallel β-sheet stabilized by two conserved disulfide bonds. The stability of each of the three A21 loops is provided by hydrogen bonds between main-chain atoms and several highly conserved residues, making the overall fold of A21 and its orthologs resilient to evolutionary change. Based on AlphaFold modeling and phylogenetic analysis of A21, we suggest that its highly conserved N-terminal transmembrane domain and C-terminal α-helix enable A21 integration into EFC, where it primarily interacts with the G3/L5 subcomplex and the smallest of EFC components, the O3 protein.

Organizational Affiliation

Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Ceva Innovation Center GmbH, Am Pharmapark, 06861 Dessau-Rosslau, Germany.

Macromolecule Content

Total Structure Weight: 70.89 kDa
Atom Count: 3,686
Modeled Residue Count: 448
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion membrane protein A21	A, B, C, D, E A, B, C, D, E, F	94	Vaccinia virus Western Reserve	Mutation(s): 0 Gene Names: MVA131L
UniProt
Find proteins for P68711 (Vaccinia virus (strain Ankara)) Explore P68711 Go to UniProtKB: P68711
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68711
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain SB [auth F] SDF format, chain RA [auth C] MOL2 format, chain SB [auth F] MOL2 format, chain RA [auth C] mmCIF format, chain SB [auth F] mmCIF format, chain RA [auth C]	RA [auth C], SB [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain RA [auth C] Focus chain SB [auth F] Interactions & Density Focus chain RA [auth C] Focus chain SB [auth F]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] SDF format, chain N [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain N [auth A]	AA [auth B] BA [auth B] CA [auth B] M [auth A] N [auth A] AA [auth B], BA [auth B], CA [auth B], M [auth A], N [auth A], O [auth A], OA [auth C], X [auth B], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
PG0 Query on PG0 Download Ideal Coordinates CCD File SDF format, chain GA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain GA [auth B]	GA [auth B]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Interactions & Density Focus chain GA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain SA [auth C] SDF format, chain TB [auth F] MOL2 format, chain BB [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain TB [auth F] mmCIF format, chain BB [auth D] mmCIF format, chain SA [auth C] mmCIF format, chain TB [auth F]	BB [auth D], SA [auth C], TB [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain SA [auth C] Focus chain TB [auth F] Interactions & Density Focus chain BB [auth D] Focus chain SA [auth C] Focus chain TB [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain JB [auth F] SDF format, chain KB [auth F] MOL2 format, chain CB [auth E] MOL2 format, chain JB [auth F] MOL2 format, chain KB [auth F] mmCIF format, chain CB [auth E] mmCIF format, chain JB [auth F] mmCIF format, chain KB [auth F]	CB [auth E], JB [auth F], KB [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth E] Focus chain JB [auth F] Focus chain KB [auth F] Interactions & Density Focus chain CB [auth E] Focus chain JB [auth F] Focus chain KB [auth F]
DHL Query on DHL Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain UB [auth F] MOL2 format, chain HA [auth B] MOL2 format, chain UB [auth F] mmCIF format, chain HA [auth B] mmCIF format, chain UB [auth F]	HA [auth B], UB [auth F]	2-AMINO-ETHANETHIOL C₂ H₇ N S UFULAYFCSOUIOV-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain UB [auth F] Interactions & Density Focus chain HA [auth B] Focus chain UB [auth F]
PGR Query on PGR Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	R-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-GSVOUGTGSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
PDO Query on PDO Download Ideal Coordinates CCD File SDF format, chain HB [auth E] SDF format, chain NA [auth C] SDF format, chain V [auth B] SDF format, chain WA [auth D] SDF format, chain U [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain NA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain HB [auth E] mmCIF format, chain NA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain U [auth B]	HB [auth E], NA [auth C], U [auth B], V [auth B], WA [auth D]	1,3-PROPANDIOL C₃ H₈ O₂ YPFDHNVEDLHUCE-UHFFFAOYSA-N		Interactions Focus chain HB [auth E] Focus chain NA [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth D] Interactions & Density Focus chain HB [auth E] Focus chain NA [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain EB [auth E] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain T [auth B] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain FB [auth E] SDF format, chain MB [auth F] MOL2 format, chain EB [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain FB [auth E] MOL2 format, chain MB [auth F] mmCIF format, chain EB [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain FB [auth E] mmCIF format, chain MB [auth F]	EB [auth E] FB [auth E] H [auth A] I [auth A] IA [auth C] EB [auth E], FB [auth E], H [auth A], I [auth A], IA [auth C], JA [auth C], KA [auth C], MB [auth F], T [auth B], UA [auth D], VA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EB [auth E] Focus chain FB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain MB [auth F] Focus chain T [auth B] Focus chain UA [auth D] Focus chain VA [auth D] Interactions & Density Focus chain EB [auth E] Focus chain FB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain MB [auth F] Focus chain T [auth B] Focus chain UA [auth D] Focus chain VA [auth D]
POL Query on POL Download Ideal Coordinates CCD File SDF format, chain XA [auth D] MOL2 format, chain XA [auth D] mmCIF format, chain XA [auth D]	XA [auth D]	N-PROPANOL C₃ H₈ O BDERNNFJNOPAEC-UHFFFAOYSA-N		Interactions Focus chain XA [auth D] Interactions & Density Focus chain XA [auth D]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain IB [auth E] MOL2 format, chain IB [auth E] mmCIF format, chain IB [auth E]	IB [auth E]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain IB [auth E] Interactions & Density Focus chain IB [auth E]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain DB [auth E] SDF format, chain G [auth A] SDF format, chain LB [auth F] SDF format, chain S [auth B] SDF format, chain TA [auth D] MOL2 format, chain DB [auth E] MOL2 format, chain G [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth D] mmCIF format, chain DB [auth E] mmCIF format, chain G [auth A] mmCIF format, chain LB [auth F] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth D]	DB [auth E], G [auth A], LB [auth F], S [auth B], TA [auth D]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain G [auth A] Focus chain LB [auth F] Focus chain S [auth B] Focus chain TA [auth D] Interactions & Density Focus chain DB [auth E] Focus chain G [auth A] Focus chain LB [auth F] Focus chain S [auth B] Focus chain TA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QB [auth F] SDF format, chain R [auth A] SDF format, chain RB [auth F] MOL2 format, chain AB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth F] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth F] mmCIF format, chain AB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth F] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth F]	AB [auth D] DA [auth B] EA [auth B] P [auth A] PA [auth C] AB [auth D], DA [auth B], EA [auth B], P [auth A], PA [auth C], Q [auth A], QB [auth F], R [auth A], RB [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QB [auth F] Focus chain R [auth A] Focus chain RB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QB [auth F] Focus chain R [auth A] Focus chain RB [auth F]
MOH Query on MOH Download Ideal Coordinates CCD File SDF format, chain GB [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NB [auth F] SDF format, chain OB [auth F] SDF format, chain PB [auth F] MOL2 format, chain GB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain OB [auth F] MOL2 format, chain PB [auth F] mmCIF format, chain GB [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain OB [auth F] mmCIF format, chain PB [auth F]	GB [auth E] J [auth A] K [auth A] L [auth A] LA [auth C] GB [auth E], J [auth A], K [auth A], L [auth A], LA [auth C], MA [auth C], NB [auth F], OB [auth F], PB [auth F]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain GB [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain PB [auth F] Interactions & Density Focus chain GB [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain PB [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain QA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain QA [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain QA [auth C]	FA [auth B], QA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain QA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain QA [auth C]