3IT8

Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein

PDB DOI: https://doi.org/10.2210/pdb3IT8/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Yaba-like disease virus
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2009-08-27 Released: 2009-10-20
Deposition Author(s): Yang, Z., West Jr., A.P., Bjorkman, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.266
R-Value Work: 0.236
R-Value Observed: 0.236

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of TNFalpha complexed with a poxvirus MHC-related TNF binding protein

Yang, Z., West, A.P., Bjorkman, P.J.

(2009) Nat Struct Mol Biol 16: 1189-1191

PubMed: 19838188 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nsmb.1683
Primary Citation of Related Structures:
3IT8

PubMed Abstract:
The poxvirus 2L protein binds tumor necrosis factor-alpha (TNFalpha) to inhibit host antiviral and immune responses. The 2.8-A 2L-TNFalpha structure reveals three symmetrically arranged 2L molecules per TNFalpha trimer. 2L resembles class I major histocompatibility complex (MHC) molecules but lacks a peptide-binding groove and beta2-microglobulin light chain. Overlap between the 2L and host TNF receptor-binding sites on TNFalpha rationalizes 2L inhibition of TNFalpha-TNF receptor interactions and prevention of TNFalpha-induced immune responses.

Organizational Affiliation

Division of Biology 114-96, California Institute of Technology, Pasadena, California, USA.

Macromolecule Content

Total Structure Weight: 335.67 kDa
Atom Count: 22,002
Modelled Residue Count: 2,706
Deposited Residue Count: 2,910
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A, B, C, G, H A, B, C, G, H, I	161	Homo sapiens	Mutation(s): 0 Gene Names: TNF
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens) Explore P01375 Go to UniProtKB: P01375
PHAROS: P01375 GTEx: ENSG00000232810
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01375
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2L protein	D, E, F, J, K D, E, F, J, K, L	324	Yaba-like disease virus	Mutation(s): 0 Gene Names: 2L
UniProt
Find proteins for Q9DHW0 (Yaba-like disease virus) Explore Q9DHW0 Go to UniProtKB: Q9DHW0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9DHW0
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain D Focus chain E Focus chain F Focus chain J Focus chain K Focus chain L
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 BA [auth L] SDF format, chain CA [auth L] SDF format, chain DA [auth L] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain W [auth J] SDF format, chain X [auth J] SDF format, chain Y [auth K] SDF format, chain Z [auth K] SDF format, chain AA [auth K] SDF format, chain R [auth E] SDF format, chain V [auth J] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth L] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain W [auth J] MOL2 format, chain X [auth J] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth K] MOL2 format, chain AA [auth K] MOL2 format, chain R [auth E] MOL2 format, chain V [auth J] mmCIF format, chain BA [auth L] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth L] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain W [auth J] mmCIF format, chain X [auth J] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth K] mmCIF format, chain AA [auth K] mmCIF format, chain R [auth E] mmCIF format, chain V [auth J]	AA [auth K] BA [auth L] CA [auth L] DA [auth L] M [auth D] AA [auth K], BA [auth L], CA [auth L], DA [auth L], M [auth D], N [auth D], O [auth D], P [auth E], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth F], V [auth J], W [auth J], X [auth J], Y [auth K], Z [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.266
R-Value Work: 0.236
R-Value Observed: 0.236
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.656	α = 90
b = 170.295	β = 92.04
c = 122.002	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
Web-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Yang, Z.

West Jr., A.P.

Bjorkman, P.J.

Revision History (Full details and data files)

Version 1.0: 2009-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2015-12-09
Changes: Database references
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.5: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-11-06
Changes: Structure summary

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3IT8

Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein

Crystal structure of TNFalpha complexed with a poxvirus MHC-related TNF binding protein

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt