[English] 日本語
Yorodumi
- PDB-1mhc: MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mhc
TitleMODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION
Components
  • (MHC CLASS I ANTIGEN H2-M3) x 2
  • NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
KeywordsHISTOCOMPATIBILITY ANTIGEN/PEPTIDE / HISTOCOMPATIBILITY ANTIGEN-PEPTIDE complex
Function / homology
Function and homology information


Complex I biogenesis / Mitochondrial translation termination / alpha-beta T cell activation involved in immune response / Respiratory electron transport / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / TAP2 binding / TAP1 binding / positive regulation of natural killer cell mediated cytotoxicity / Endosomal/Vacuolar pathway ...Complex I biogenesis / Mitochondrial translation termination / alpha-beta T cell activation involved in immune response / Respiratory electron transport / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / TAP2 binding / TAP1 binding / positive regulation of natural killer cell mediated cytotoxicity / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to hydroperoxide / regulation of membrane depolarization / NADH:ubiquinone reductase (H+-translocating) / beta-2-microglobulin binding / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / TAP binding / respiratory chain complex I / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / NADH dehydrogenase (ubiquinone) activity / cellular defense response / Neutrophil degranulation / 14-3-3 protein binding / aerobic respiration / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / mitochondrial membrane / positive regulation of type II interferon production / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / positive regulation of nitric oxide biosynthetic process / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein refolding / protein-folding chaperone binding / cellular response to lipopolysaccharide / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / response to hypoxia / defense response to bacterium / mitochondrial inner membrane / defense response to Gram-positive bacterium / immune response / response to xenobiotic stimulus / receptor ligand activity / signaling receptor binding / Golgi membrane / external side of plasma membrane / innate immune response / lysosomal membrane / neuronal cell body / dendrite / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / NADH-ubiquinone oxidoreductase chain 1 / Histocompatibility 2, M region locus 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsWang, C.-R. / Fischer Lindahl, K. / Deisenhofer, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3
Authors: Wang, C.R. / Castano, A.R. / Peterson, P.A. / Slaughter, C. / Lindahl, K.F. / Deisenhofer, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1991
Title: H-2M3 Encodes the Mhc Class I Molecule Presenting the Maternally Transmitted Antigen of the Mouse
Authors: Wang, C.-R. / Loveland, B.E. / Fischer Lindahl, K.
History
DepositionAug 23, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC CLASS I ANTIGEN H2-M3
B: MHC CLASS I ANTIGEN H2-M3
C: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
D: MHC CLASS I ANTIGEN H2-M3
E: MHC CLASS I ANTIGEN H2-M3
F: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2427
Polymers91,0216
Non-polymers2211
Water6,702372
1
A: MHC CLASS I ANTIGEN H2-M3
B: MHC CLASS I ANTIGEN H2-M3
C: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)45,5103
Polymers45,5103
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-27 kcal/mol
Surface area19540 Å2
MethodPISA
2
D: MHC CLASS I ANTIGEN H2-M3
E: MHC CLASS I ANTIGEN H2-M3
F: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7324
Polymers45,5103
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-24 kcal/mol
Surface area19420 Å2
MethodPISA
3
D: MHC CLASS I ANTIGEN H2-M3
E: MHC CLASS I ANTIGEN H2-M3
F: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
hetero molecules

A: MHC CLASS I ANTIGEN H2-M3
B: MHC CLASS I ANTIGEN H2-M3
C: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)91,2427
Polymers91,0216
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_444x-1,y-1,z-11
Buried area10450 Å2
ΔGint-49 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.250, 66.100, 55.170
Angle α, β, γ (deg.)102.71, 96.28, 110.19
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 210 / 2: CIS PROLINE - PRO B 32 / 3: CIS PROLINE - PRO D 210 / 4: CIS PROLINE - PRO E 32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9585, -0.1906, 0.2119), (-0.2302, -0.9561, 0.1812), (0.1681, -0.2225, -0.9603)4.9129, 38.8128, 28.6944
2given(0.9641, -0.1867, 0.1886), (-0.2217, -0.9573, 0.1854), (0.1459, -0.2206, -0.9644)4.8695, 38.7328, 28.6928
3given(0.9646, -0.1991, 0.1729), (-0.2317, -0.953, 0.1953), (0.1259, -0.2284, -0.9654)4.9692, 38.6988, 28.6453
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 D 2 .. D 182 A 2 .. A 182 0.288 M2 D 183 .. D 275 A 183 .. A 275 0.292 M3 E 1 .. E 99 B 1 .. B 99 0.312

-
Components

#1: Protein MHC CLASS I ANTIGEN H2-M3 / MAJOR HISTOCOMPATIBILITY COMPLEX


Mass: 32650.650 Da / Num. of mol.: 2 / Mutation: INS(275(A)-282(A)), INS(275(D)-282(D))
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3 B2M / Gene (production host): H2-M3 B2M / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q31093
#2: Protein MHC CLASS I ANTIGEN H2-M3 / MAJOR HISTOCOMPATIBILITY COMPLEX


Mass: 11704.359 Da / Num. of mol.: 2 / Mutation: INS(275(A)-282(A)), INS(275(D)-282(D))
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3 B2M / Gene (production host): H2-M3 B2M / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887
#3: Protein/peptide NONAPEPTIDE FROM RAT NADH DEHYDROGENASE / ND1


Mass: 1155.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P03889
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 26 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
220 mMTris-HCl1drop
316-18 %PEG80001reservoir
4100 mMHEPES1reservoir
52 %MPD1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 33706 / % possible obs: 70 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / % possible obs: 43 %

-
Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.19 --
obs0.19 33706 70 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 14 372 6668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.88
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more