[English] 日本語
Yorodumi
- PDB-7tuc: Crystal structure of HLA-B*44:05 (T73C) with 9mer EEFGRAFSF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tuc
TitleCrystal structure of HLA-B*44:05 (T73C) with 9mer EEFGRAFSF
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • MHC class II antigen peptide
KeywordsIMMUNE SYSTEM / tapasin / histocompatibility complex class I / MHC-I / HLA / peptide editing / peptide loading complex / PLC / antigen presentation / immune response
Function / homology
Function and homology information


antigen processing and presentation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway ...antigen processing and presentation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Beta-2-Microglobulin / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Beta-2-Microglobulin / 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
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsJiang, J. / Natarajan, K. / Kim, E. / Boyd, L.F. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation.
Authors: Jiang, J. / Taylor, D.K. / Kim, E.J. / Boyd, L.F. / Ahmad, J. / Mage, M.G. / Truong, H.V. / Woodward, C.H. / Sgourakis, N.G. / Cresswell, P. / Margulies, D.H. / Natarajan, K.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
P: MHC class II antigen peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1448
Polymers44,7743
Non-polymers3705
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-7 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.750, 82.582, 110.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B alpha chain


Mass: 31804.158 Da / Num. of mol.: 1 / Mutation: T73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B44:05 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

-
Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MHC class II antigen peptide


Mass: 1090.165 Da / Num. of mol.: 1 / Fragment: EEFGRAFSF
Source method: isolated from a genetically manipulated source
Details: HLA-DPA1*02:01 derived peptide 9mer / Source: (gene. exp.) Synthetic construct (others) / Gene: HLA-DPA1 / Production host: Synthetic construct (others) / References: UniProt: Q9TQB0

-
Non-polymers , 3 types, 459 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 16% PEG 3350, 0.1M Tris, 0.2M Ca Acetate / PH range: 6.0-8.5

-
Data collection

DiffractionMean temperature: 273 K / Ambient temp details: LN blow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→46.03 Å / Num. obs: 128295 / % possible obs: 95.43 % / Redundancy: 2 % / Biso Wilson estimate: 9.5 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0329 / Rpim(I) all: 0.0329 / Rrim(I) all: 0.0465 / Net I/σ(I): 11.61
Reflection shellResolution: 1.25→1.295 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4125 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11969 / CC1/2: 0.555 / CC star: 0.845 / Rpim(I) all: 0.4125 / Rrim(I) all: 0.5834 / % possible all: 80.29

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6O

1m6o


Resolution: 1.25→46.03 Å / SU ML: 0.1071 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.0858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 1936 1.57 %
Rwork0.1796 121482 -
obs0.1799 123418 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.53 Å2
Refinement stepCycle: LAST / Resolution: 1.25→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 24 454 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423283
X-RAY DIFFRACTIONf_angle_d0.80624456
X-RAY DIFFRACTIONf_chiral_restr0.0826454
X-RAY DIFFRACTIONf_plane_restr0.0077588
X-RAY DIFFRACTIONf_dihedral_angle_d13.08641232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.26061140.27346977X-RAY DIFFRACTION77.58
1.28-1.320.26521280.23928013X-RAY DIFFRACTION89.09
1.32-1.350.2471320.23288271X-RAY DIFFRACTION91.77
1.35-1.40.26081320.22938314X-RAY DIFFRACTION92.6
1.4-1.450.20181370.198610X-RAY DIFFRACTION95.19
1.45-1.510.19711400.17558682X-RAY DIFFRACTION96.33
1.51-1.570.18571410.16648795X-RAY DIFFRACTION97.73
1.57-1.660.18291410.16268921X-RAY DIFFRACTION98.61
1.66-1.760.20011440.17449020X-RAY DIFFRACTION99.26
1.76-1.90.21181440.17299026X-RAY DIFFRACTION99.45
1.9-2.090.18641430.16719077X-RAY DIFFRACTION99.57
2.09-2.390.18941440.17149134X-RAY DIFFRACTION99.73
2.39-3.010.19091460.18729208X-RAY DIFFRACTION99.79
3.01-46.030.17151500.16519434X-RAY DIFFRACTION98.8
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)
11.42654366084-0.522739648750.2039509526851.256032973860.02659041333030.6676822104450.06078712606040.0940459195657-0.110481310214-0.0714893095367-0.04852536126770.1159693990380.0411678092489-0.0783280363657-0.008218526186380.0585302296297-0.00500325960964-0.01316776461320.0505826491858-0.01290021230240.0615012283654-10.20956882075.7543262714-30.7662412001
21.41958780584-0.04577488241660.2233279596190.5741765226740.05143716668260.39673559732-0.007930339853450.1298323734490.111174961526-0.0580698804951-0.0111044426979-0.032495474312-0.02687110874110.01547868592870.01227490753590.0637330292850.00300771307882-0.00161962311820.05086246483080.01020445184720.0517133759394-0.30754361061116.3093042207-31.0281544107
30.4530251730720.0726139304822-0.4694655073350.6125550042740.0700085501292.807849489460.0211982720278-0.10715652756-0.01376172737290.1366856823680.02993949389380.0321116946727-0.148877672791-0.0353841072218-0.02658962238050.08353597952430.01268148128460.007360984590510.09894173595620.0002544498237540.0715666770613-25.232455191415.7189073303-3.8331306691
47.890947621451.903230714020.5673297718722.34398455905-0.0743096062942.037137449430.0137361044969-0.186097828715-0.2313257826780.0372110552007-0.073222774639-0.0918963868127-0.07786070561220.1850071819620.06117454168290.0892858968230.005631185446970.007184772811480.0872340739550.02634454821180.0625443735065-9.732920841683.52678597193-8.98693952742
55.124561766652.89068262428-1.482873660061.6743848964-0.6613710681351.12722789233-0.06503644064240.124500180133-0.03921358068740.1160477115340.1422780980990.5952454929050.257828016944-0.640547371926-0.1066371425820.130078776192-0.03702836385360.04879062739240.2022853148140.04474154804570.290079469175-32.1758109534-1.74964652977-10.0167109748
66.08207430493.40860336077-1.550463185933.54317413979-0.7251023971322.11841934737-0.05733404516230.012829884108-0.0368032533206-0.09533183252350.006986825633920.2643661616780.108366593959-0.1509502111550.05300119112220.0639547148010.00475548505226-0.004332131512160.04437723876530.006100833645560.083896916228-17.73535712230.34268354296-13.1180813751
76.970428578136.47747152896-3.211538300617.08880972886-2.563721974272.26910364835-0.4296860336870.0545887764441-0.453518285333-0.3608872330460.179916537032-0.2275968204970.302148524006-0.009069420149190.2221846522980.134320362030.01498601194320.04167313911770.08536385753120.02633665948520.140200446232-8.56776694742-4.84936801611-13.6452127648
82.693952815410.7019711771690.16333940783.256535385011.050880055380.340684318192-0.1557280615130.0257629122101-0.481912097934-0.2360637735220.04566901827210.1729884735230.4056670785590.07541711231070.07309694918160.262006687731-0.001367192130620.05291389779350.0999429795853-0.0124102128330.226608800246-17.2670658262-11.8902541169-15.0836149918
97.683490839064.524318304040.8407597155365.673650652891.87748364870.72709383767-0.05272891654830.427042452164-0.248159710986-0.3332064131940.1559898783490.1809105598720.506346314457-0.0493928534569-0.1048621023390.181924768729-0.00598832098619-0.04183184180280.0902270703811-0.006751824323670.0758125934391-9.671651818245.29088872076-22.4499045128
104.176370674882.37791651058-1.361492364782.9023138966-1.0656914221.69997551091-0.00420479945888-0.03372011267140.0436528956304-0.103396712266-0.01285313999580.250276498250.0480023875608-0.05954088642910.01960655283270.07512131676020.007624017484080.005544140132680.0468017693641-0.01173915994090.0789624641439-13.65685012212.96433341829-16.6098892792
110.7273838866410.799491375787-0.2780817461661.2061832584-0.8101167647390.8838132891790.0316469084252-0.605094445666-0.4129999399550.3083263127950.008665364243960.36644807540.300753055885-0.349841586462-0.03774738323480.35948350705-0.06994065623940.1267185853030.3276234953950.08970095598340.37846766824-28.0273800395-11.0979441482-2.58218217464
120.353893201517-0.46213319257-0.3062794906180.6880323250940.1117697219011.249234394030.018594868259-0.282305704073-0.3986102004150.230096035443-0.148940930067-0.2049784808240.1488513784240.197404603520.05391040520020.1483402545450.03114902997480.01194652808080.1557155998360.1128533699030.206888190914-7.20319428997-5.76593606168-7.32160776284
135.60422642685-1.33127226096-0.04547998245533.39321712114-0.2101681536663.53961745151-0.145454557745-0.624808989727-0.3434111460720.455484594365-0.03787745297960.1907953524470.05153676204350.01247689604980.1571935087080.212158024899-0.009581466087670.05898308563660.1942608614150.04495175175450.142158560125-19.8818054919-2.07289919048-2.32660538518
147.200930829670.4502138863172.481506430421.060453077240.04011307029341.51339072461-0.03887118874050.6164035290570.296284058076-0.0898971076033-0.0198353854287-0.1255687921360.02898856768870.162649656230.08192165351260.1376335430430.0127326219070.009284380891030.1414226608270.01315425788730.117895250226-0.086174013448515.1243549409-37.1733229695
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 56 )AA1 - 561 - 56
22chain 'A' and (resid 57 through 174 )AA57 - 17457 - 174
33chain 'A' and (resid 175 through 274 )AA175 - 274175 - 274
44chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
55chain 'B' and (resid 12 through 19 )BB12 - 1912 - 19
66chain 'B' and (resid 20 through 30 )BB20 - 3020 - 30
77chain 'B' and (resid 31 through 41 )BB31 - 4131 - 41
88chain 'B' and (resid 42 through 51 )BB42 - 5142 - 51
99chain 'B' and (resid 52 through 56 )BB52 - 5652 - 56
1010chain 'B' and (resid 57 through 71 )BB57 - 7157 - 71
1111chain 'B' and (resid 72 through 77 )BB72 - 7772 - 77
1212chain 'B' and (resid 78 through 90 )BB78 - 9078 - 90
1313chain 'B' and (resid 91 through 99 )BB91 - 9991 - 99
1414chain 'P' and (resid 1 through 9 )PC1 - 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