6A3V | pdb_00006a3v

Complex structure of human 4-1BB and 4-1BBL

PDB DOI: https://doi.org/10.2210/pdb6A3V/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Baculovirus transfer vector pFASTBAC1
Mutation(s): No

Deposited: 2018-06-17 Released: 2018-10-10
Deposition Author(s): Li, Y., Zhang, C., Chai, Y., Qi, J., Tien, P., Gao, S., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free:
0.293 (Depositor), 0.290 (DCC)
R-Value Work:
0.264 (Depositor), 0.260 (DCC)
R-Value Observed:
0.265 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Limited Cross-Linking of 4-1BB by 4-1BB Ligand and the Agonist Monoclonal Antibody Utomilumab.

Li, Y., Tan, S., Zhang, C., Chai, Y., He, M., Zhang, C.W., Wang, Q., Tong, Z., Liu, K., Lei, Y., Liu, W.J., Liu, Y., Tian, Z., Cao, X., Yan, J., Qi, J., Tien, P., Gao, S., Gao, G.F.

(2018) Cell Rep 25: 909-920.e4

PubMed: 30355497 Search on PubMed
DOI: https://doi.org/10.1016/j.celrep.2018.09.073
Primary Citation of Related Structures:
6A3V, 6A3W

PubMed Abstract:
Monoclonal antibodies (mAbs) targeting the co-stimulatory molecule 4-1BB are of interest for tumor immunotherapy. We determined the complex structures of human 4-1BB with 4-1BB ligand (4-1BBL) or utomilumab to elucidate the structural basis of 4-1BB activation. The 4-1BB/4-1BBL complex displays a typical TNF/TNFR family binding mode. The structure of utomilumab/4-1BB complex shows that utomilumab binds to dimeric 4-1BB with a distinct but partially overlapping binding area with 4-1BBL. Competitive binding analysis demonstrates that utomilumab blocks the 4-1BB/4-1BBL interaction, indicating the interruption of ligand-mediated signaling. The binding profiles of 4-1BBL and utomilumab to monomeric or dimeric 4-1BB indicate limited cross-linking of 4-1BB molecules. These findings provide mechanistic insight into the binding of 4-1BB with its ligand and its agonist mAb, which may facilitate the future development of anti-4-1BB biologics for tumor immunotherapy.

Organizational Affiliation

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China.

CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

ImmuFuCell Biotechnology, Beijing 100102, China.

Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

University of Chinese Academy of Sciences, Beijing 100049, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.

Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.

Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China.

Institute of Immunology, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, China.

Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China.

CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China. Electronic address: gaos@sibet.ac.cn.

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China. Electronic address: gaof@im.ac.cn.

Macromolecule Content

Total Structure Weight: 471.15 kDa
Atom Count: 25,073
Modeled Residue Count: 3,342
Deposited Residue Count: 4,392
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 9	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	203	Homo sapiens	Mutation(s): 0 Gene Names: TNFSF9
UniProt & NIH Common Fund Data Resources
Find proteins for P41273 (Homo sapiens) Explore P41273 Go to UniProtKB: P41273
PHAROS: P41273 GTEx: ENSG00000125657
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41273
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 9	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	163	Homo sapiens	Mutation(s): 0 Gene Names: TNFRSF9, CD137, ILA
UniProt & NIH Common Fund Data Resources
Find proteins for Q07011 (Homo sapiens) Explore Q07011 Go to UniProtKB: Q07011
PHAROS: Q07011 GTEx: ENSG00000049249
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q07011
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F Focus chain H Focus chain J Focus chain L Focus chain N Focus chain P Focus chain R Focus chain T Focus chain V Focus chain X	Go to GlyGen: Q07011-1
Sequence Annotations Expand
Reference Sequence

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 AA [auth F] SDF format, chain BA [auth H] SDF format, chain CA [auth J] SDF format, chain DA [auth L] SDF format, chain EA [auth N] SDF format, chain FA [auth P] SDF format, chain GA [auth R] SDF format, chain HA [auth T] SDF format, chain IA [auth V] SDF format, chain JA [auth X] SDF format, chain Y [auth B] SDF format, chain Z [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth J] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth N] MOL2 format, chain FA [auth P] MOL2 format, chain GA [auth R] MOL2 format, chain HA [auth T] MOL2 format, chain IA [auth V] MOL2 format, chain JA [auth X] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth J] mmCIF format, chain DA [auth L] mmCIF format, chain EA [auth N] mmCIF format, chain FA [auth P] mmCIF format, chain GA [auth R] mmCIF format, chain HA [auth T] mmCIF format, chain IA [auth V] mmCIF format, chain JA [auth X] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth D]	AA [auth F] BA [auth H] CA [auth J] DA [auth L] EA [auth N] AA [auth F], BA [auth H], CA [auth J], DA [auth L], EA [auth N], FA [auth P], GA [auth R], HA [auth T], IA [auth V], JA [auth X], Y [auth B], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth J] Focus chain DA [auth L] Focus chain EA [auth N] Focus chain FA [auth P] Focus chain GA [auth R] Focus chain HA [auth T] Focus chain IA [auth V] Focus chain JA [auth X] Focus chain Y [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth J] Focus chain DA [auth L] Focus chain EA [auth N] Focus chain FA [auth P] Focus chain GA [auth R] Focus chain HA [auth T] Focus chain IA [auth V] Focus chain JA [auth X] Focus chain Y [auth B] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free: 0.293 (Depositor), 0.290 (DCC)
R-Value Work: 0.264 (Depositor), 0.260 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.091	α = 90
b = 137.195	β = 111.8
c = 140.318	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-10
Type: Initial release
Version 1.1: 2019-04-24
Changes: Data collection, Database references, Structure summary
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-10-23
Changes: Structure summary