PDB-3t6q: Crystal structure of mouse RP105/MD-1 complex

ID or keywords:

Entry

Database: PDB / ID: 3t6q

Title

Crystal structure of mouse RP105/MD-1 complex

Components

CD180 antigen
Lymphocyte antigen 86

Keywords

IMMUNE SYSTEM / Protein-Protein complex / Leucine rich repeat / MD-2 related lipid recognition / receptor / innate immunity / glycosylation

Function / homology

Function and homology information

Toll Like Receptor 4 (TLR4) Cascade / B cell proliferation involved in immune response / positive regulation of lipopolysaccharide-mediated signaling pathway / toll-like receptor signaling pathway / lipopolysaccharide-mediated signaling pathway / extracellular matrix / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / membrane => GO:0016020 / inflammatory response ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.9 Å

Authors

Ohto, U. / Shimizu, T.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Crystal Structures of Mouse and Human RP105/MD-1 Complexes Reveal Unique Dimer Organization of the Toll-Like Receptor Family.
Authors: Ohto, U. / Miyake, K. / Shimizu, T.

History

Deposition	Jul 28, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3t6q.cif.gz	616.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3t6q_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	3t6q_full_validation.pdf.gz	2.3 MB	Display
Data in XML	3t6q_validation.xml.gz	70.2 KB	Display
Data in CIF	3t6q_validation.cif.gz	100.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t6/3t6q ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t6q	HTTPS FTP

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Related structure data

Related structure data	3b2dC C: citing same article (ref.)
Similar structure data	3rg1-4 3rg1-1 3b2d-d 3rg1-2 3ujp-1 7asc-d 3rit-d 7daw-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (9) #248 - Aug 2020 Phytosulfokine Receptor similarity (4) #68 - Aug 2005 Neurotrophins similarity (4) #105 - Sep 2008 Ribonuclease A similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: CD180 antigen

C: Lymphocyte antigen 86

B: CD180 antigen

D: Lymphocyte antigen 86

hetero molecules

177 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	143.753, 192.790, 75.799
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-1- CU

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Protein , 2 types, 4 molecules ABCD

#1: Protein	CD180 antigen / Lymphocyte antigen 78 / Ly-78 / Radioprotective 105 kDa protein Mass: 67986.031 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-626 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd180, Ly78, Rp105 / Cell (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q62192
#2: Protein	Lymphocyte antigen 86 / Ly-86 / Protein MD-1 Mass: 16202.112 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ly86, Md1 / Cell (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: O88188

#1: Protein

CD180 antigen / Lymphocyte antigen 78 / Ly-78 / Radioprotective 105 kDa protein

Mass: 67986.031 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Cd180, Ly78, Rp105 / Cell (production host): S2 / Production host:

Drosophila (fruit flies) / References: UniProt: Q62192

#2: Protein

Lymphocyte antigen 86 / Ly-86 / Protein MD-1

Mass: 16202.112 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Ly86, Md1 / Cell (production host): S2 / Production host:

Drosophila (fruit flies) / References: UniProt: O88188

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Sugars , 4 types, 18 molecules

#3: Polysaccharide

alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...

Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-h1_f2-g1_h2-i1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}	LINUCS	PDB-CARE

#4: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

#5: Polysaccharide

alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...

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Protein , 2 types, 4 molecules ABCD

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Sugars , 4 types, 18 molecules

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-Assembly

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-Protein , 2 types, 4 molecules ABCD

-Sugars , 4 types, 18 molecules

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Assembly

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Components

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Protein , 2 types, 4 molecules ABCD

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Sugars , 4 types, 18 molecules