[English] 日本語
Yorodumi
- PDB-3cc5: H-2Db complex with human gp100 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cc5
TitleH-2Db complex with human gp100
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • nonameric peptide from Melanocyte protein Pmel 17
KeywordsIMMUNE SYSTEM / murine MHC / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted / Melanin biosynthesis
Function / homology
Function and homology information


positive regulation of melanin biosynthetic process / cis-Golgi network membrane / melanin biosynthetic process / melanosome membrane / multivesicular body, internal vesicle / melanosome organization / multivesicular body membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of melanin biosynthetic process / cis-Golgi network membrane / melanin biosynthetic process / melanosome membrane / multivesicular body, internal vesicle / melanosome organization / multivesicular body membrane / 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 / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / melanosome / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / MHC class I, alpha chain, C-terminal ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Melanocyte protein PMEL
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBadia-Martinez, D. / Achour, A.
CitationJournal: Cancer Res. / Year: 2009
Title: Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100.
Authors: van Stipdonk, M.J. / Badia-Martinez, D. / Sluijter, M. / Offringa, R. / van Hall, T. / Achour, A.
History
DepositionFeb 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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: nonameric peptide from Melanocyte protein Pmel 17
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: nonameric peptide from Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,74015
Polymers89,8996
Non-polymers8419
Water10,935607
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: nonameric peptide from Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4188
Polymers44,9493
Non-polymers4685
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-39 kcal/mol
Surface area19020 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: nonameric peptide from Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3227
Polymers44,9493
Non-polymers3724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-41 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.200, 165.400, 161.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
51A
61D
12A
22D
32A
42D
52A
62D
72A
82D
13B
23E
14C
24F

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
111HISHISVALVAL1AA3 - 343 - 34
211HISHISVALVAL1DD3 - 343 - 34
321PHEPHELEULEU1AA36 - 7836 - 78
421PHEPHELEULEU1DD36 - 7836 - 78
531ASNASNGLYGLY1AA80 - 17580 - 175
631ASNASNGLYGLY1DD80 - 17580 - 175
112THRTHRPROPRO1AA182 - 193182 - 193
212THRTHRPROPRO1DD182 - 193182 - 193
322METMETPROPRO1AA228 - 276228 - 276
422METMETPROPRO1DD228 - 276228 - 276
532GLUGLUASPASP2AA223 - 227223 - 227
632GLUGLUASPASP2DD223 - 227223 - 227
742SERSERGLUGLU1AA195 - 222195 - 222
842SERSERGLUGLU1DD195 - 222195 - 222
113LYSLYSMETMET1BB3 - 993 - 99
213LYSLYSMETMET1EE3 - 993 - 99
114LYSLYSLEULEU1CC1 - 91 - 9
214LYSLYSLEULEU1FF1 - 91 - 9

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 2 types, 4 molecules ADBE

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


Mass: 32087.703 Da / Num. of mol.: 2 / Fragment: Extracellular part, UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide nonameric peptide from Melanocyte protein Pmel 17 / Silver locus protein homolog / Melanocyte lineage-specific antigen GP100 / Melanoma-associated ME20 ...Silver locus protein homolog / Melanocyte lineage-specific antigen GP100 / Melanoma-associated ME20 antigen / ME20M / ME20-M


Mass: 1157.321 Da / Num. of mol.: 2 / Fragment: Extracellular part, UNP residues 25-33 / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: P40967

-
Non-polymers , 3 types, 616 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 6000, 0.1M Ammonium sulfate, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 4, 2007
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.91→24.82 Å / Num. all: 71103 / Num. obs: 66186 / % possible obs: 93.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.91→2 Å / % possible all: 65.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N5A

1n5a


Resolution: 1.91→24.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.688 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.195 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 3432 5 %RANDOM
Rwork0.22762 ---
all0.2351 66190 --
obs0.22972 64542 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.891 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.91→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 51 607 6994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216574
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9448924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65123.626342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.717151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1191550
X-RAY DIFFRACTIONr_chiral_restr0.1110.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025144
X-RAY DIFFRACTIONr_nbd_refined0.250.32930
X-RAY DIFFRACTIONr_nbtor_refined0.3210.54448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.5889
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.358
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.532
X-RAY DIFFRACTIONr_mcbond_it1.16923935
X-RAY DIFFRACTIONr_mcangle_it1.82236208
X-RAY DIFFRACTIONr_scbond_it1.15723089
X-RAY DIFFRACTIONr_scangle_it1.77632716
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1420tight positional0.040.05
2A733tight positional0.040.05
3B804tight positional0.040.05
4C82tight positional0.030.05
2A21medium positional0.420.5
1A1420tight thermal0.150.5
2A733tight thermal0.130.5
3B804tight thermal0.130.5
4C82tight thermal0.150.5
2A21medium thermal0.262
LS refinement shellResolution: 1.912→1.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 193 -
Rwork0.277 3759 -
obs--77.87 %

+
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