4G8A

Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS

PDB DOI: https://doi.org/10.2210/pdb4G8A/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Drosophila
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2012-07-23 Released: 2012-10-17
Deposition Author(s): Ohto, U., Shimizu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.249
R-Value Work: 0.199
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I

Ohto, U., Yamakawa, N., Akashi-Takamura, S., Miyake, K., Shimizu, T.

(2012) J Biol Chem 287: 40611-40617

PubMed: 23055527 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.404608
Primary Citation of Related Structures:
4G8A

PubMed Abstract:
TLR4 polymorphism replacing Asp-299 with Gly and Thr-399 with Ile (D299G/T399I) causes LPS hyporesponsiveness.

Organizational Affiliation

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.

Macromolecule Content

Total Structure Weight: 184.51 kDa
Atom Count: 12,381
Modelled Residue Count: 1,486
Deposited Residue Count: 1,558
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 4	A, B	635	Homo sapiens	Mutation(s): 2 Gene Names: TLR4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O00206 (Homo sapiens) Explore O00206 Go to UniProtKB: O00206
PHAROS: O00206 GTEx: ENSG00000136869
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00206
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen 96	C, D	144	Homo sapiens	Mutation(s): 1 Gene Names: LY96, ESOP1, MD2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6Y9 (Homo sapiens) Explore Q9Y6Y9 Go to UniProtKB: Q9Y6Y9
PHAROS: Q9Y6Y9 GTEx: ENSG00000154589
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6Y9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LP5 Query on LP5 Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain S [auth D] MOL2 format, chain M [auth C] MOL2 format, chain S [auth D]	M [auth C], S [auth D]	(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE C₃₄ H₆₆ N O₁₂ P HEHQDWUWJVPREQ-XQJZMFRCSA-N		Interactions Focus chain M [auth C] Focus chain S [auth D] Interactions & Density Focus chain M [auth C] Focus chain S [auth D]
LP4 Query on LP4 Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain R [auth D] MOL2 format, chain L [auth C] MOL2 format, chain R [auth D]	L [auth C], R [auth D]	2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose C₃₄ H₆₆ N O₁₂ P AJRPJFBMHCTNGK-XQJZMFRCSA-N		Interactions Focus chain L [auth C] Focus chain R [auth D] Interactions & Density Focus chain L [auth C] Focus chain R [auth D]
KDO Query on KDO Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain V [auth D] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D]	P [auth C], V [auth D]	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid C₈ H₁₄ O₈ NNLZBVFSCVTSLA-HXUQBWEZSA-N		Interactions Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain P [auth C] Focus chain V [auth D]
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain U [auth D]	O [auth C], U [auth D]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain O [auth C] Focus chain U [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain Q [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain Q [auth D]	I [auth A], J [auth B], K [auth C], Q [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain Q [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain Q [auth D]
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain T [auth D] MOL2 format, chain N [auth C] MOL2 format, chain T [auth D]	N [auth C], T [auth D]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain T [auth D] Interactions & Density Focus chain N [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.249
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.038	α = 90
b = 124.68	β = 115.72
c = 109.14	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-17

Deposition Author(s):

Ohto, U.

Shimizu, T.

Revision History (Full details and data files)

Version 1.0: 2012-10-17
Type: Initial release
Version 1.1: 2013-09-04
Changes: Database references, Non-polymer description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4G8A

Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS

Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2