[English] 日本語
Yorodumi
- PDB-6ei2: Crystal Structure of HLA-A68 presenting a C-terminally extended p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ei2
TitleCrystal Structure of HLA-A68 presenting a C-terminally extended peptide
Components
  • Beta-2-microglobulin
  • G1/S-specific cyclin-D2
  • HLA class I histocompatibility antigen, A-68 alpha chain
KeywordsIMMUNE SYSTEM / C-terminally extended peptide / HLA
Function / homology
Function and homology information


cyclin D2-CDK4 complex / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Drug-mediated inhibition of CDK4/CDK6 activity / cellular response to X-ray / cyclin-dependent protein serine/threonine kinase activator activity / Regulation of RUNX1 Expression and Activity / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation ...cyclin D2-CDK4 complex / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Drug-mediated inhibition of CDK4/CDK6 activity / cellular response to X-ray / cyclin-dependent protein serine/threonine kinase activator activity / Regulation of RUNX1 Expression and Activity / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / TAP binding / endoplasmic reticulum exit site / cyclin-dependent protein kinase holoenzyme complex / detection of bacterium / 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 / beta-2-microglobulin binding / long-term memory / adult locomotory behavior / positive regulation of G1/S transition of mitotic cell cycle / T cell receptor binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of T cell mediated cytotoxicity / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / G1/S transition of mitotic cell cycle / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / positive regulation of type II interferon production / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / 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 epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of protein phosphorylation / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / T cell receptor signaling pathway / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Cyclin D associated events in G1 / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / E3 ubiquitin ligases ubiquitinate target proteins / nuclear membrane / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / cell division / focal adhesion
Similarity search - Function
Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma ...Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 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
: / : / NICKEL (II) ION / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / G1/S-specific cyclin-D2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsPicaud, S. / Guillaume, P. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gfeller, D. / Filippakopoulos, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust095751/Z/11/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal Structure of HLA-A68 presenting a C-terminally extended peptide
Authors: Picaud, S. / Guillaume, P. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gfeller, D. / Filippakopoulos, P.
History
DepositionSep 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry
Revision 1.2Oct 16, 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, A-68 alpha chain
B: Beta-2-microglobulin
C: G1/S-specific cyclin-D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,77015
Polymers44,9383
Non-polymers83212
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex (HLA-A*68 : B2M : peptide)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-46 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.061, 80.247, 110.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-68 alpha chain / Aw-68 / HLA class I histocompatibility antigen / A-28 alpha chain / MHC class I antigen A*68


Mass: 31969.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET24(+) Vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P01891, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 Vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: P61769

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide G1/S-specific cyclin-D2


Mass: 1089.216 Da / Num. of mol.: 1 / Fragment: UNP residues 114-123 / Source method: obtained synthetically / Details: C-terminally extended peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P30279

-
Non-polymers , 5 types, 454 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#7: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG3350 0.005M cobalt chloride 0.005M cadmium chloride 0.005M nickel chloride 0.005M magnesium chloride 0.1M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.61→29.531 Å / Num. all: 68846 / Num. obs: 68846 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Rsym value: 0.094 / Net I/av σ(I): 5.4 / Net I/σ(I): 11.3 / Num. measured all: 454107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.61-1.76.60.6021.398730.2530.6540.60299.5
1.7-1.86.70.4211.894080.1760.4570.421100
1.8-1.926.60.2842.688520.1190.3080.284100
1.92-2.086.60.184482650.0770.20.184100
2.08-2.286.60.1345.376320.0560.1450.134100
2.28-2.556.70.116.369340.0460.1190.11100
2.55-2.946.70.0867.661390.0360.0940.086100
2.94-3.66.60.0649.352440.0270.070.064100
3.6-5.096.40.05610.741260.0240.060.056100
5.09-29.5315.90.0579.823730.0250.0620.05799.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å29.53 Å
Translation3.5 Å29.53 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
SCALA3.3.22data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 4HWZ, 5T6X, 4RMU, 4HWZ

4hwz

5t6x

4rmu

4hwz


Resolution: 1.61→29.53 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.37 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0678 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 1917 2.8 %RANDOM
Rwork0.1579 ---
obs0.1586 66856 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.77 Å2 / Biso mean: 20.343 Å2 / Biso min: 9.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.61→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 29 442 3602
Biso mean--34.11 30.46 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193273
X-RAY DIFFRACTIONr_bond_other_d0.0020.022864
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9264437
X-RAY DIFFRACTIONr_angle_other_deg1.03536638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83723.295173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9631529
X-RAY DIFFRACTIONr_chiral_restr0.1160.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
LS refinement shellResolution: 1.61→1.652 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 117 -
Rwork0.219 4822 -
all-4939 -
obs--98.66 %
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)
10.17510.0252-0.04750.1375-0.11720.1337-0.0206-0.0158-0.002-0.0217-0.0206-0.04260.0199-0.02550.04120.0050.00540.00460.0659-0.00640.022848.362743.564620.9237
20.3794-0.20950.58390.7278-0.70991.1605-0.04430.00660.02330.10510.0090.0167-0.1177-0.00040.03530.02150.00550.00220.03950.00980.026950.668344.674239.9641
30.8649-0.6855-0.48220.76320.31260.3119-0.0142-0.04320.0324-0.10390.0388-0.01760.02510.0197-0.02460.0633-0.0075-0.00870.05470.00290.023753.446158.6249.1478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 299
2X-RAY DIFFRACTION2B20 - 119
3X-RAY DIFFRACTION3C10 - 19

+
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