6MYY

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map

PDB DOI: https://doi.org/10.2210/pdb6MYY/pdb
EM Map EMD-9294: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-11-02 Released: 2018-11-14
Deposition Author(s): Borst, A.J., Weidle, C.E., Gray, M.D., Frenz, B., Snijder, J., Joyce, M.G., Georgiev, I.S., Stewart-Jones, G.B.E., Kwong, P.D., McGuire, A.T., DiMaio, F., Stamatatos, L., Pancera, M., Veesler, D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 391.97 kDa
Atom Count: 20,139
Modelled Residue Count: 2,307
Deposited Residue Count: 3,264
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
426c DS-SOSIP D3	A, D [auth B], G [auth E]	626	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for M4Q8P8 (Human immunodeficiency virus 1) Explore M4Q8P8 Go to UniProtKB: M4Q8P8
Find proteins for Q2N0S9 (Human immunodeficiency virus 1) Explore Q2N0S9 Go to UniProtKB: Q2N0S9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q2N0S9M4Q8P8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC01GL light chain	B [auth L], E [auth C], H [auth F]	229	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6PJF2 (Homo sapiens) Explore Q6PJF2 Go to UniProtKB: Q6PJF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PJF2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC01GL heavy chain	C [auth H], F [auth D], I [auth G]	233	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6C4S0 (Homo sapiens) Explore S6C4S0 Go to UniProtKB: S6C4S0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S6C4S0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	GA [auth g], IA [auth i], J [auth I], JA [auth j], K [auth J], GA [auth g], IA [auth i], J [auth I], JA [auth j], K [auth J], KA [auth k], LA [auth l], MA [auth m], S, U, UA [auth u], V, W, WA [auth w], X, XA [auth x], Y, YA [auth y]	2		N-Glycosylation	Interactions Focus chain GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain JA [auth j] Focus chain K [auth J] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain S Focus chain U Focus chain UA [auth u] Focus chain V Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Interactions & Density Focus chain GA [auth g] Focus chain IA [auth i] Focus chain J [auth I] Focus chain JA [auth j] Focus chain K [auth J] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain S Focus chain U Focus chain UA [auth u] Focus chain V Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K], NA [auth n], Z	5		N-Glycosylation	Interactions Focus chain L [auth K] Focus chain NA [auth n] Focus chain Z Interactions & Density Focus chain L [auth K] Focus chain NA [auth n] Focus chain Z
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], M, OA [auth o]	6		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain M Focus chain OA [auth o] Interactions & Density Focus chain AA [auth a] Focus chain M Focus chain OA [auth o]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], DA [auth d], EA [auth e], N, P, BA [auth b], DA [auth d], EA [auth e], N, P, PA [auth p], Q, RA [auth r], SA [auth s]	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain N Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain RA [auth r] Focus chain SA [auth s] Interactions & Density Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain N Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain RA [auth r] Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], O, QA [auth q]	7		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain O Focus chain QA [auth q] Interactions & Density Focus chain CA [auth c] Focus chain O Focus chain QA [auth q]
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f], R, TA [auth t]	4		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain R Focus chain TA [auth t] Interactions & Density Focus chain FA [auth f] Focus chain R Focus chain TA [auth t]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], T, VA [auth v]	5		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain T Focus chain VA [auth v] Interactions & Density Focus chain HA [auth h] Focus chain T Focus chain VA [auth v]
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain BB [auth A] SDF format, chain CB [auth A] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain GB [auth B] SDF format, chain HB [auth E] SDF format, chain IB [auth E] SDF format, chain JB [auth E] SDF format, chain KB [auth E] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain IB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain KB [auth E] MOL2 format, chain ZA [auth A]	AB [auth A] BB [auth A] CB [auth A] DB [auth B] EB [auth B] AB [auth A], BB [auth A], CB [auth A], DB [auth B], EB [auth B], FB [auth B], GB [auth B], HB [auth E], IB [auth E], JB [auth E], KB [auth E], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain ZA [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	C [auth H], F [auth D], I [auth G]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	Rosetta

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Stewart-Jones, G.B.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM120553

Revision History (Full details and data files)

Version 1.0: 2018-11-14
Type: Initial release
Version 1.1: 2018-11-21
Changes: Data collection, Database references
Version 2.0: 2020-01-08
Changes: Author supporting evidence, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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6MYY

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)