[English] 日本語
Yorodumi
- PDB-5w69: HLA-C*06:02 presenting ARFNDLRFV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w69
TitleHLA-C*06:02 presenting ARFNDLRFV
Components
  • ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, Cw-6 alpha chain
KeywordsIMMUNE SYSTEM / HLA / Antigen presentation / Human Leukocyte Antigen
Function / homology
Function and homology information


peripheral nervous system neuron development / RUNX3 regulates RUNX1-mediated transcription / core-binding factor complex / positive regulation of CD8-positive, alpha-beta T cell differentiation / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates BCL2L11 (BIM) transcription / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX3 regulates WNT signaling / response to transforming growth factor beta / RUNX3 regulates YAP1-mediated transcription ...peripheral nervous system neuron development / RUNX3 regulates RUNX1-mediated transcription / core-binding factor complex / positive regulation of CD8-positive, alpha-beta T cell differentiation / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates BCL2L11 (BIM) transcription / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX3 regulates WNT signaling / response to transforming growth factor beta / RUNX3 regulates YAP1-mediated transcription / RUNX3 Regulates Immune Response and Cell Migration / RUNX3 regulates NOTCH signaling / RUNX3 regulates CDKN1A transcription / negative regulation of cell cycle / regulation of cell differentiation / TAP binding / hemopoiesis / RUNX3 regulates p14-ARF / 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 / chondrocyte differentiation / ossification / negative regulation of receptor binding / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / transcription corepressor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / Regulation of RUNX3 expression and activity / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / neuron differentiation / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / learning or memory / protein phosphorylation / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / endoplasmic reticulum lumen / DNA-binding transcription factor activity / Amyloid fiber formation / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle
Similarity search - Function
Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / MHC class I, alpha chain, C-terminal ...Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / 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
HLA class I histocompatibility antigen, C alpha chain / Beta-2-microglobulin / Runt-related transcription factor 3 / HLA class I histocompatibility antigen, C alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMobbs, J.I. / Vivian, J.P. / Rossjohn, J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule.
Authors: Mobbs, J.I. / Illing, P.T. / Dudek, N.L. / Brooks, A.G. / Baker, D.G. / Purcell, A.W. / Rossjohn, J. / Vivian, J.P.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, Cw-6 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, Cw-6 alpha chain
D: Beta-2-microglobulin
E: HLA class I histocompatibility antigen, Cw-6 alpha chain
F: Beta-2-microglobulin
G: HLA class I histocompatibility antigen, Cw-6 alpha chain
H: Beta-2-microglobulin
I: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
J: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
K: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL
L: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)180,42312
Polymers180,42312
Non-polymers00
Water13,872770
1
A: HLA class I histocompatibility antigen, Cw-6 alpha chain
B: Beta-2-microglobulin
I: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-15 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, Cw-6 alpha chain
D: Beta-2-microglobulin
J: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-14 kcal/mol
Surface area18420 Å2
MethodPISA
3
E: HLA class I histocompatibility antigen, Cw-6 alpha chain
F: Beta-2-microglobulin
K: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-17 kcal/mol
Surface area18600 Å2
MethodPISA
4
G: HLA class I histocompatibility antigen, Cw-6 alpha chain
H: Beta-2-microglobulin
L: ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Theoretical massNumber of molelcules
Total (without water)45,1063
Polymers45,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-14 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.182, 182.137, 222.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
HLA class I histocompatibility antigen, Cw-6 alpha chain / MHC class I antigen Cw*6


Mass: 32087.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q29963, UniProt: P10321*PLUS
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide
ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL


Mass: 1139.307 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q13761*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M Na acetate and 20 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→74.34 Å / Num. obs: 52631 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 51.22 Å2 / Rpim(I) all: 0.11 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 9.2 % / Num. unique obs: 4512 / Rpim(I) all: 0.51 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT6

4nt6


Resolution: 2.8→40.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / Rfactor Rfree error: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2671 5.08 %RANDOM
Rwork0.164 ---
obs0.167 52539 100 %-
Displacement parametersBiso mean: 34.86 Å2
Baniso -1Baniso -2Baniso -3
1--7.5189 Å20 Å20 Å2
2--5.8439 Å20 Å2
3---1.675 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.8→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12458 0 0 795 13253
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112831HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1117458HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4355SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes364HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1876HARMONIC5
X-RAY DIFFRACTIONt_it12831HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion18.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1571SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14305SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 183 4.76 %
Rwork0.211 3665 -
all0.216 3848 -
obs--100 %
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)
11.2874-0.296-0.23271.2875-0.03782.8525-0.0270.1044-0.0512-0.2094-0.0487-0.12510.391-0.02910.0757-0.0671-0.040.0448-0.1123-0.0189-0.04579.9448-56.8992-22.032
23.37171.318-1.43173.6046-0.83822.73710.0184-0.05740.06660.06040.0021-0.0975-0.02010.2102-0.0206-0.09990.00680.0240.07090.003-0.154116.4536-32.0175-47.7354
31.0038-0.84240.71931.7429-2.04714.0285-0.0682-0.02270.09780.09730.17770.1351-0.5434-0.5401-0.1095-0.05530.05150.03440.00920.0171-0.0591-0.7206-34.5311-33.6411
41.04050.39580.06983.3803-1.26753.47520.1683-0.1368-0.1729-0.04420.06990.47610.52970.0896-0.2382-0.12380.027-0.0648-0.214-0.04170.0542-6.0751-56.2223-89.5292
53.5212-1.1102-0.8423.90460.75452.4939-0.01570.12870.0146-0.033-0.00190.1206-0.0837-0.08690.0176-0.0978-0.01970.01390.04640.048-0.1436-11.7641-31.4653-63.4878
61.45260.57181.5491.65581.93284.4589-0.05760.0692-0.0401-0.0250.0251-0.076-0.18830.50410.0324-0.1093-0.02470.02710.0258-0.0052-0.03175.5093-34.5094-77.467
71.24440.06070.5043.15950.2651.2057-0.0201-0.04250.046-0.11060.2439-0.5442-0.15730.1686-0.2238-0.0747-0.0660.1233-0.1428-0.1136-0.0137-7.098.1527-95.1786
82.93991.29640.70095.07792.52463.9554-0.09270.17220.0696-0.27710.1463-0.0201-0.19540.1226-0.0537-0.09090.03810.037-0.09910.0095-0.0444-4.7636-25.9382-107.131
91.1153-0.4723-0.76724.79380.05012.5632-0.13390.0031-0.49560.12890.34420.54420.2551-0.1483-0.2102-0.1405-0.05330.0467-0.1623-0.02040.1253-20.6168-15.3856-94.7704
104.44561.12190.84414.75750.98471.30390.133-0.0708-0.1306-0.30920.07610.2306-0.0135-0.2238-0.20910.0325-0.1309-0.1395-0.25410.1288-0.15544.96957.7815-15.8773
112.61410.14631.20122.9452-1.15931.9012-0.2735-0.24550.35870.07980.00270.1324-0.5441-0.16980.2708-0.0280.0652-0.0931-0.086-0.0925-0.04616.4854-26.9568-3.2035
121.93211.0444-0.47370.8230.21022.26620.0139-0.0234-0.1939-0.1834-0.0514-0.2227-0.48730.45560.03750.0301-0.152-0.152-0.1240.0949-0.024720.8948-14.0806-15.0741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2{ A|181 - A|274 }A181 - 274
2X-RAY DIFFRACTION3{ B|0 - B|99 }B0 - 99
3X-RAY DIFFRACTION5{ C|181 - C|274 }C181 - 274
4X-RAY DIFFRACTION6{ D|0 - D|99 }D0 - 99
5X-RAY DIFFRACTION8{ E|181 - E|274 }E181 - 274
6X-RAY DIFFRACTION9{ F|0 - F|99 }F0 - 99
7X-RAY DIFFRACTION11{ G|181 - G|274 }G181 - 274
8X-RAY DIFFRACTION12{ H|0 - H|99 }H0 - 99

+
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