[English] 日本語
Yorodumi
- PDB-1s7r: Crystal structures of the murine class I major histocompatibility... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s7r
TitleCrystal structures of the murine class I major histocompatibility complex H-2Kb in complex with LCMV-derived gp33 index peptide and three of its escape variants
Components
  • Beta-2-microglobulin
  • Glycoprotein 9-residue peptide
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / LCMV / MHC class I / immune escape
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / receptor-mediated endocytosis of virus by host cell / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / host cell endoplasmic reticulum membrane / defense response to bacterium / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / membrane / cytosol
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / H-2 class I histocompatibility antigen, K-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsVelloso, L.M. / Michaelsson, J. / Ljunggren, H.G. / Schneider, G. / Achour, A.
CitationJournal: J.Immunol. / Year: 2004
Title: Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition.
Authors: Velloso, L.M. / Michaelsson, J. / Ljunggren, H.G. / Schneider, G. / Achour, A.
History
DepositionJan 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CYSTEINE IN THE ORIGINAL SEQUENCE IS REPLACED INTENTIONALLY BY A METHIONINE TO AVOID ...SEQUENCE THE CYSTEINE IN THE ORIGINAL SEQUENCE IS REPLACED INTENTIONALLY BY A METHIONINE TO AVOID OXIDATION OF THE PEPTIDE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)103,8316
Polymers103,8316
Non-polymers00
Water1,13563
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,9163
Polymers51,9163
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-19 kcal/mol
Surface area18680 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,9163
Polymers51,9163
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-20 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.192, 88.519, 120.026
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
51A
61D
71A
81D
91A
101D
111A
121D
131A
141D
151A
161D
171A
181D
191A
201D
211A
221D
231A
241D
251A
261D
271A
281D
291A
301D
311A
321D
12B
22E
32B
42E
52B
62E
72B
82E
92B
102E
112B
122E
132B
142E
152B
162E
172B
182E
192B
202E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPRO1AA1 - 21 - 2
211GLYGLYPROPRO1DD1 - 21 - 2
321SERSERSERSER1AA4 - 924 - 92
421SERSERSERSER1DD4 - 924 - 92
531THRTHRLYSLYS1AA94 - 14494 - 144
631THRTHRLYSLYS1DD94 - 14494 - 144
741VALVALTHRTHR1AA189 - 190189 - 190
841VALVALTHRTHR1DD189 - 190189 - 190
951SERSERCYSCYS1AA193 - 259193 - 259
1051SERSERCYSCYS1DD193 - 259193 - 259
1161VALVALTYRTYR1AA261 - 262261 - 262
1261VALVALTYRTYR1DD261 - 262261 - 262
1371HISHISHISHIS3AA33
1471HISHISHISHIS3DD33
1581HISHISHISHIS3AA9393
1681HISHISHISHIS3DD9393
1791HISHISHISHIS3AA188188
1891HISHISHISHIS3DD188188
19101HISHISHISHIS3AA191191
20101HISHISHISHIS3DD191191
21111HISHISHISHIS3AA260260
22111HISHISHISHIS3DD260260
23121HISHISHISHIS3AA263263
24121HISHISHISHIS3DD263263
25131HISHISHISHIS3AA145145
26131HISHISHISHIS3DD145145
27141HISHISHISHIS3AA192192
28141HISHISHISHIS3DD192192
29151GLNGLNPROPRO1AA264 - 276264 - 276
30151GLNGLNPROPRO1DD264 - 276264 - 276
31161LYSLYSALAALA5AA146 - 187146 - 187
32161LYSLYSALAALA5DD146 - 187146 - 187
112ILEILEARGARG1BB1 - 121 - 12
212ILEILEARGARG1EE1 - 121 - 12
322ILEILEALAALA1BB35 - 6635 - 66
422ILEILEALAALA1EE35 - 6635 - 66
532THRTHRLYSLYS1BB68 - 8368 - 83
632THRTHRLYSLYS1EE68 - 8368 - 83
742ASPASPMETMET1BB85 - 9985 - 99
842ASPASPMETMET1EE85 - 9985 - 99
952HISHISHISHIS3BB3434
1052HISHISHISHIS3EE3434
1162HISHISHISHIS3BB6767
1262HISHISHISHIS3EE6767
1372HISHISHISHIS3BB8484
1472HISHISHISHIS3EE8484
1582HISHISHISHIS3BB1313
1682HISHISHISHIS3EE1313
1792PROPROPHEPHE1BB14 - 3014 - 30
1892PROPROPHEPHE1EE14 - 3014 - 30
19102HISHISPROPRO3BB31 - 3331 - 33
20102HISHISPROPRO3EE31 - 3331 - 33
113ALAALAMETMET1CC2 - 92 - 9
213ALAALAMETMET1FF2 - 92 - 9

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2KB


Mass: 39200.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P01887
#3: Protein/peptide Glycoprotein 9-residue peptide


Mass: 1011.215 Da / Num. of mol.: 2 / Mutation: F6L / Source method: obtained synthetically
Details: The peptide was chemically synthesized, the sequence of the peptide is naturally found in Lymphocytic choriomeningitis virus
References: UniProt: P07399
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.03 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium/potassium phosphate, Methyl pentane diol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.097 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.097 Å / Relative weight: 1
ReflectionResolution: 2.95→25 Å / Num. all: 22159 / Num. obs: 20741 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.95→3.1 Å / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N59

1n59


Resolution: 2.95→24.84 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.807 / SU B: 22.341 / SU ML: 0.425 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.505 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28961 1041 5 %RANDOM
Rwork0.23905 ---
all0.24 22159 --
obs0.24165 19684 93.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.203 Å2
Baniso -1Baniso -2Baniso -3
1-4.19 Å20 Å22.18 Å2
2---4.87 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.95→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 0 63 6339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216460
X-RAY DIFFRACTIONr_bond_other_d0.0020.025588
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9388772
X-RAY DIFFRACTIONr_angle_other_deg0.902313038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885762
X-RAY DIFFRACTIONr_chiral_restr0.0860.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027192
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021354
X-RAY DIFFRACTIONr_nbd_refined0.2230.21482
X-RAY DIFFRACTIONr_nbd_other0.2470.26981
X-RAY DIFFRACTIONr_nbtor_other0.0910.23704
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0370.21
X-RAY DIFFRACTIONr_mcbond_it0.7021.53836
X-RAY DIFFRACTIONr_mcangle_it1.33926198
X-RAY DIFFRACTIONr_scbond_it1.54932624
X-RAY DIFFRACTIONr_scangle_it2.7044.52574
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3507tight positional0.030.05
2B1477tight positional0.030.05
3C118tight positional0.020.05
1A248medium positional0.130.5
1A497loose positional0.195
2B68loose positional0.115
1A3507tight thermal0.060.5
2B1477tight thermal0.070.5
3C118tight thermal0.060.5
1A248medium thermal0.512
1A497loose thermal1.0610
2B68loose thermal0.5510
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 61
Rwork0.289 1373
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5409-0.2771-0.31650.4412-0.20040.30550.14520.0397-0.0077-0.0281-0.11210.00940.03660.0403-0.03310.11520.004-0.0380.20510.00280.2836-1.010513.965349.2604
21.52851.77570.72875.1898-0.1565-0.3190.06660.1689-0.1566-0.68890.0536-0.0349-0.21840.0027-0.12020.2260.0346-0.01370.2581-0.01580.239311.9001-18.237440.4002
32.9791-1.99290.74992.6013-1.27911.81110.0829-0.1208-0.1201-0.064-0.05870.1331-0.12450.1408-0.02410.0129-0.0161-0.05530.1748-0.010.2774.128-9.645159.3717
415.5601-5.463923.419212.72091.4726-7.2391.563-0.65391.05530.4494-0.9129-1.3938-1.1435-0.6067-0.65010.2591-0.11110.15590.2640.05560.2735-2.776220.154349.4433
50.30450.4607-0.36551.57360.11391.3801-0.02160.026-0.0357-0.0233-0.09070.02460.14940.02780.11230.48140.01590.07450.3501-0.01750.274618.7414-3.21569.0581
61.1737-0.4741-0.34844.3551-0.78911.28210.22760.01060.18230.0722-0.11540.3064-0.1574-0.0059-0.11230.2622-0.05850.02320.3583-0.02570.257919.606228.994524.6769
71.46451.2913-1.03232.23530.0212.1925-0.07110.01070.0208-0.3143-0.0832-0.1691-0.02520.13270.15430.49020.07470.04590.31340.06210.271929.82120.41536.894
811.9024-8.079823.767912.1528-23.692732.56090.86761.0741-0.6944-0.8491-0.7281-0.78991.86740.9379-0.13950.30620.0617-0.00780.36510.08330.456917.8129-9.41017.538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1821 - 182
2X-RAY DIFFRACTION2AA183 - 276183 - 276
3X-RAY DIFFRACTION3BB1 - 991 - 99
4X-RAY DIFFRACTION4CC1 - 91 - 9
5X-RAY DIFFRACTION5DD1 - 1821 - 182
6X-RAY DIFFRACTION6DD183 - 276183 - 276
7X-RAY DIFFRACTION7EE1 - 991 - 99
8X-RAY DIFFRACTION8FF1 - 91 - 9

+
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