[English] 日本語
Yorodumi
- PDB-1s7u: Crystal structures of the murine class I major histocompatibility... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s7u
TitleCrystal structures of the murine class I major histocompatibility complex H-2Db 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, D-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 / 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 ...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 / 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 / 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 / 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 / plasma 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, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.4Oct 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, D-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: Glycoprotein 9-residue peptide
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)204,79512
Polymers204,79512
Non-polymers00
Water18,3031016
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,1993
Polymers51,1993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-18 kcal/mol
Surface area19750 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,1993
Polymers51,1993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-19 kcal/mol
Surface area19530 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,1993
Polymers51,1993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-21 kcal/mol
Surface area19490 Å2
MethodPISA
4
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,1993
Polymers51,1993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-20 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.389, 123.343, 99.392
Angle α, β, γ (deg.)90.00, 103.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12B
22E
32H
42K
13C
23F
33I
43L

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTRPTRPAA1 - 2741 - 274
21GLYGLYTRPTRPDD1 - 2741 - 274
31GLYGLYTRPTRPGG1 - 2741 - 274
41PROPROTRPTRPJJ2 - 2742 - 274
12ILEILEMETMETBB1 - 991 - 99
22ILEILEMETMETEE1 - 991 - 99
32ILEILEMETMETHH1 - 991 - 99
42ILEILEMETMETKK1 - 991 - 99
13LYSLYSMETMETCC1 - 91 - 9
23LYSLYSMETMETFF1 - 91 - 9
33LYSLYSMETMETII1 - 91 - 9
43LYSLYSMETMETLL1 - 91 - 9

NCS ensembles :
ID
1
2
3

-
Components

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


Mass: 38449.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 4
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: 1045.232 Da / Num. of mol.: 4 / 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.: 1016 / 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: 3.13 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, Tris , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→72.7 Å / Num. all: 109867 / Num. obs: 108769 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.42 Å / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N5A

1n5a


Resolution: 2.2→72.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.285 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26222 5426 5 %RANDOM
Rwork0.21327 ---
obs0.21569 103314 99 %-
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: 25.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.01 Å2
2--0.49 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→72.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12577 0 0 1016 13593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02112963
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211106
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9317596
X-RAY DIFFRACTIONr_angle_other_deg0.784325925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3351517
X-RAY DIFFRACTIONr_chiral_restr0.0790.21774
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214443
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022765
X-RAY DIFFRACTIONr_nbd_refined0.1890.22484
X-RAY DIFFRACTIONr_nbd_other0.2340.212958
X-RAY DIFFRACTIONr_nbtor_other0.0850.27957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2769
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.249
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.2217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.239
X-RAY DIFFRACTIONr_mcbond_it0.6061.57639
X-RAY DIFFRACTIONr_mcangle_it1.148212321
X-RAY DIFFRACTIONr_scbond_it1.36835324
X-RAY DIFFRACTIONr_scangle_it2.3274.55275
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4229medium positional0.510.5
12D4229medium positional0.510.5
13G4229medium positional0.580.5
14J4229medium positional0.420.5
21B1527medium positional0.480.5
22E1527medium positional0.330.5
23H1527medium positional0.420.5
24K1527medium positional0.370.5
31C137medium positional0.590.5
32F137medium positional0.70.5
33I137medium positional0.850.5
34L137medium positional0.960.5
11A4229medium thermal0.322
12D4229medium thermal0.352
13G4229medium thermal0.362
14J4229medium thermal0.332
21B1527medium thermal0.42
22E1527medium thermal0.312
23H1527medium thermal0.372
24K1527medium thermal0.372
31C137medium thermal0.342
32F137medium thermal0.372
33I137medium thermal0.492
34L137medium thermal0.42
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.318 377
Rwork0.27 6880
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)
10.8613-0.32960.74370.99960.19451.2443-0.02920.2730.02580.03970.0671-0.1083-0.01280.218-0.03790.1223-0.06950.05760.2157-0.01250.185-5.284-3.24526.689
21.58850.74712.02381.53061.91953.3336-0.08240.16570.0006-0.15110.1602-0.0736-0.12470.1284-0.07770.0907-0.08790.02690.25110.00020.106-2.68310.65440.755
322.4355-4.423-4.27992.74751.55226.37990.2683-0.3571-0.3865-0.69-0.03-0.0301-0.19460.2918-0.23830.2566-0.07630.07250.2036-0.01640.1922-13.3930.5028.41
40.6843-0.16440.28811.70160.04141.443-0.06180.1511-0.03820.24990.0851-0.26310.06680.1512-0.02330.1571-0.00940.00880.1054-0.0440.205931.39956.34775.226
52.7831.52542.92.69822.81425.6885-0.07680.07940.03260.08550.2079-0.1246-0.13840.4135-0.13110.1736-0.03570.0060.171-0.02560.135734.93470.12589.273
612.3092-6.0224-2.64763.58060.87772.6870.15790.402-0.0921-0.3357-0.0064-0.1559-0.1223-0.0103-0.15150.194-0.06850.03550.1953-0.02840.177524.35360.60456.839
71.9016-0.3811-0.58521.8641-0.04141.14780.10660.07320.166-0.2782-0.0319-0.3772-0.03040.2431-0.07460.18380.01510.04030.2412-0.03620.1753-3.51987.23623.88
84.8754-1.0891-4.6071.07452.11434.9909-0.01970.3013-0.28250.03190.00140.04990.0299-0.02990.01830.14990.1262-0.0050.3708-0.03910.17631.8372.81110.623
915.05742.2913-2.60710.7209-1.68242.9911-0.0725-0.7872-0.71120.2760.0616-0.2177-0.04680.13770.01090.18810.0487-0.02240.1715-0.00750.1453-12.64283.05541.357
101.76750.3007-0.53521.311-0.04380.9815-0.0563-0.0328-0.04250.030.1102-0.35080.01410.0789-0.05390.13390.0706-0.05950.0688-0.04690.246129.71723.44172.825
113.1418-1.0351-2.57770.88481.08323.3207-0.2306-0.0191-0.25970.08420.0310.07010.26070.21720.19970.14920.07290.02690.1732-0.02980.162333.739.40359.175
1244.87984.97750.18454.35560.7079-1.48030.6403-1.51250.35830.9254-0.1326-0.37640.02590.0289-0.50770.32090.0828-0.09050.2055-0.01430.19620.36919.79590.075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2741 - 274
2X-RAY DIFFRACTION2BB1 - 991 - 99
3X-RAY DIFFRACTION3CC1 - 91 - 9
4X-RAY DIFFRACTION4DD1 - 2741 - 274
5X-RAY DIFFRACTION5EE1 - 991 - 99
6X-RAY DIFFRACTION6FF1 - 91 - 9
7X-RAY DIFFRACTION7GG1 - 2741 - 274
8X-RAY DIFFRACTION8HH1 - 991 - 99
9X-RAY DIFFRACTION9II1 - 91 - 9
10X-RAY DIFFRACTION10JJ2 - 2742 - 274
11X-RAY DIFFRACTION11KK1 - 991 - 99
12X-RAY DIFFRACTION12LL1 - 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