6MGP

Structure of human 4-1BB / 4-1BBL complex

• PDB DOI: https://doi.org/10.2210/pdb6MGP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-09-14 Released: 2018-11-14 
• Deposition Author(s): Kimberlin, C.R., Chin, S.M., Roe-Zurz, Z., Xu, A., Yang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.250 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Structure of the 4-1BB/4-1BBL complex and distinct binding and functional properties of utomilumab and urelumab

Kimberlin, C.R., Chin, S.M., Roe-Zurz, Z., Zhang, P., Xu, A., Liao-Chan, S., Debasish, S., Nager, A.R., Schirle Oakdale, N., Brown, C., Wang, F., Yang, Y., Lindquist, K., Yeung, Y.A., Salek-Ardakani, S., Chaparro-Riggers, J.

(2018) Nat Commun 9: 4679-4691

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 115.64 kDa 
• Atom Count: 6,717 
• Modelled Residue Count: 885 
• Deposited Residue Count: 1,053 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor ligand superfamily member 9	A, B, C	207	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 9	D [auth X], E [auth Y], F [auth Z]	144	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q07011-1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D], H [auth E], I [auth F]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G63564LA GlyCosmos:  G63564LA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	L [auth B], M [auth C], Q [auth Z], R [auth Z]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	J [auth A], K [auth A], N [auth C], O [auth X], P [auth Y]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.250 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.013	α = 90
b = 229.378	β = 90
c = 114.9	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Kimberlin, C.R., Chin, S.M., Roe-Zurz, Z., Xu, A., Yang, Y.

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary