7mlm

Crystal structure of mouse TLR4/MD-2 in complex with sulfatides

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Toll-like receptor 4,Variable lymphocyte receptor B

Eptatretus burgeri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 4	Lymphocyte antigen 96 × 2 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 6 water × 4	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 2	Lymphocyte antigen 96 × 1 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4G1L2_EPTBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 561–635； UniProt 126–200

Toll-like receptor 4,Variable lymphocyte receptor B

Eptatretus burgeri

UniProt Q9QUK6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 4	Lymphocyte antigen 96 × 2 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 6 water × 4	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 2	Lymphocyte antigen 96 × 1 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TLR4_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 42–560； UniProt 26–544

Lymphocyte antigen 96

Mus musculus

UniProt Q9JHF9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4 其他Polymer 4	Toll-like receptor 4,Variable lymphocyte receptor B × 2 （Q4G1L2,Q9QUK6） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 6 water × 4	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2 其他Polymer 2	Toll-like receptor 4,Variable lymphocyte receptor B × 1 （Q4G1L2,Q9QUK6） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LY96_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 42–183； UniProt 19–160

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7mlm
Deposition date deposition_date	2021-04-28
Structure title title	Crystal structure of mouse TLR4/MD-2 in complex with sulfatides
Keywords keywords	Innate immunity, endogenous ligands, Toll-like receptors, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7mlm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7mlm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7mlm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.86 Å
Rg (electron density)	39.28 Å
Total Rg	39.51 Å
Atom count	12182
Residues	1452
Excluded volume	219460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7mlm__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7mlm__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Toll-like receptor 4,Variable lymphocyte receptor B
Molecular weight formula_weight	71649.8 kDa
EC 编号 ec_number	3.2.2.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6361

MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADPNPCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT

Source Source

Source organism organism	Eptatretus burgeri
Common name common_name	Inshore hagfish
NCBI taxonomy ID ncbi_taxonomy_id	7764
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Lymphocyte antigen 96
Molecular weight formula_weight	21304.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADPEKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNLFISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAEAIAGDTEEKLFCLNFTIIHRRDVNLVPRG

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	627.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide
Molecular weight formula_weight	780.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	262

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Unit-cell length a length_a	145.094 Å
Unit-cell length b length_b	164.293 Å
Unit-cell length c length_c	89.296 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.104 Å
Low-resolution limit resolution_low	46.396 Å
R factor r_factor	0.2112
R_work r_work	0.2097
R_free r_free	0.2438

Crystal structure of mouse TLR4/MD-2 in complex with sulfatides

1. Protein Identity and Related Structures Protein Identity & Related Structures

Toll-like receptor 4,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Toll-like receptor 4,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Lymphocyte antigen 96

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7mlm__assembly_1__model_1

7mlm__assembly_1__model_1 | I(q)

7mlm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of mouse TLR4/MD-2 in complex with sulfatides

1. Protein Identity and Related Structures Protein Identity & Related Structures

Toll-like receptor 4,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Toll-like receptor 4,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lymphocyte antigen 96

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7mlm__assembly_1__model_1

7mlm__assembly_1__model_1 | I(q)

7mlm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)