[English] 日本語
Yorodumi
- PDB-7q98: MHC Class I A02 Allele presenting NLSALGIFST -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q98
TitleMHC Class I A02 Allele presenting NLSALGIFST
Components
  • ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / IMP2 / Diabetes / Autoimmunity
Function / homology
Function and homology information


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 / 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 / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway ...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 / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / ER to Golgi transport vesicle membrane / 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 / recycling endosome membrane / specific granule lumen / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / 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 / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsRizkallah, P.J. / Sewell, A.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
Title: Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy.
Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. ...Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. / Legut, M. / Attaf, M. / Hopkins, J.R. / Behiry, E. / Zabkiewicz, J. / Alvares, C. / Lloyd, A. / Rogers, A. / Henley, P. / Fegan, C. / Ottmann, O. / Man, S. / Crowther, M.D. / Donia, M. / Svane, I.M. / Cole, D.K. / Brown, P.E. / Rizkallah, P. / Sewell, A.K.
History
DepositionNov 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
D: MHC class I antigen
E: Beta-2-microglobulin
F: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
G: MHC class I antigen
H: Beta-2-microglobulin
I: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
J: MHC class I antigen
K: Beta-2-microglobulin
L: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
M: MHC class I antigen
N: Beta-2-microglobulin
O: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,12255
Polymers224,26415
Non-polymers3,85740
Water8,413467
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4259
Polymers44,8533
Non-polymers5736
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,20417
Polymers44,8533
Non-polymers1,35114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,75812
Polymers44,8533
Non-polymers9059
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: MHC class I antigen
K: Beta-2-microglobulin
L: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4499
Polymers44,8533
Non-polymers5966
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: MHC class I antigen
N: Beta-2-microglobulin
O: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2858
Polymers44,8533
Non-polymers4325
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.247, 169.693, 248.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11D-306-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13A
23J
14A
24M
15B
25E
16B
26H
17B
27K
18B
28N
19D
29G
110D
210J
111D
211M
112E
212H
113E
213K
114E
214N
115G
215J
116G
216M
117H
217K
118H
218N
119J
219M
120K
220N

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODD1 - 2761 - 276
12GLYGLYPROPROAA1 - 2761 - 276
22GLYGLYPROPROGG1 - 2761 - 276
13GLYGLYPROPROAA1 - 2761 - 276
23GLYGLYPROPROJJ1 - 2761 - 276
14GLYGLYPROPROAA1 - 2761 - 276
24GLYGLYPROPROMM1 - 2761 - 276
15METMETMETMETBB0 - 991 - 100
25METMETMETMETEE0 - 991 - 100
16METMETMETMETBB0 - 991 - 100
26METMETMETMETHH0 - 991 - 100
17METMETMETMETBB0 - 991 - 100
27METMETMETMETKK0 - 991 - 100
18METMETMETMETBB0 - 991 - 100
28METMETMETMETNN0 - 991 - 100
19GLYGLYPROPRODD1 - 2761 - 276
29GLYGLYPROPROGG1 - 2761 - 276
110GLYGLYPROPRODD1 - 2761 - 276
210GLYGLYPROPROJJ1 - 2761 - 276
111GLYGLYPROPRODD1 - 2761 - 276
211GLYGLYPROPROMM1 - 2761 - 276
112METMETMETMETEE0 - 991 - 100
212METMETMETMETHH0 - 991 - 100
113METMETMETMETEE0 - 991 - 100
213METMETMETMETKK0 - 991 - 100
114METMETMETMETEE0 - 991 - 100
214METMETMETMETNN0 - 991 - 100
115GLYGLYPROPROGG1 - 2761 - 276
215GLYGLYPROPROJJ1 - 2761 - 276
116GLYGLYPROPROGG1 - 2761 - 276
216GLYGLYPROPROMM1 - 2761 - 276
117METMETMETMETHH0 - 991 - 100
217METMETMETMETKK0 - 991 - 100
118METMETMETMETHH0 - 991 - 100
218METMETMETMETNN0 - 991 - 100
119GLYGLYPROPROJJ1 - 2761 - 276
219GLYGLYPROPROMM1 - 2761 - 276
120METMETMETMETKK0 - 991 - 100
220METMETMETMETNN0 - 991 - 100

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

-
Components

-
Protein , 2 types, 10 molecules ADGJMBEHKN

#1: Protein
MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

-
Protein/peptide , 1 types, 5 molecules CFILO

#3: Protein/peptide
ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR


Mass: 1022.154 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 507 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 8000, 0.2 M Ammonium Sulphate, Sodium Cacodylate buffer 0.1 M, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.5→85 Å / Num. obs: 85745 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.04 / Rrim(I) all: 0.096 / Net I/σ(I): 10 / Num. measured all: 479533 / Scaling rejects: 91
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.550.5232480344080.8740.2410.577397.2
13.23-84.850.03235846400.9990.0160.03612.697.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.08 Å84.8 Å
Translation2.08 Å84.8 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HG1

3hg1


Resolution: 2.5→85 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 21.23 / SU ML: 0.239 / SU R Cruickshank DPI: 0.6261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 4344 5.1 %RANDOM
Rwork0.2347 ---
obs0.2367 81381 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173 Å2 / Biso mean: 46.178 Å2 / Biso min: 12.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å2-0 Å2
2--1.44 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 2.5→85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15815 0 226 467 16508
Biso mean--75.11 35.31 -
Num. residues----1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01316515
X-RAY DIFFRACTIONr_bond_other_d0.0010.01514662
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.65522376
X-RAY DIFFRACTIONr_angle_other_deg1.1841.58433760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57951925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75321.271016
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.498152655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98915143
X-RAY DIFFRACTIONr_chiral_restr0.0630.22010
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024115
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A84760.12
12D84760.12
21A87240.08
22G87240.08
31A87590.08
32J87590.08
41A86900.09
42M86900.09
51B30090.11
52E30090.11
61B30650.08
62H30650.08
71B30610.09
72K30610.09
81B30640.1
82N30640.1
91D85920.11
92G85920.11
101D85650.11
102J85650.11
111D85100.12
112M85100.12
121E31030.09
122H31030.09
131E30560.11
132K30560.11
141E30230.12
142N30230.12
151G88150.08
152J88150.08
161G87660.09
162M87660.09
171H30530.09
172K30530.09
181H30460.09
182N30460.09
191J87650.09
192M87650.09
201K30700.09
202N30700.09
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 311 -
Rwork0.29 5955 -
all-6266 -
obs--98.57 %
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)
12.50390.64610.31656.0876-2.46112.09950.5301-0.3645-0.71280.6857-0.8381-1.171-0.01660.77630.3080.5488-0.0937-0.23220.5150.29460.431644.033429.8790.7172
24.24421.95074.46853.2321.86317.58120.04460.2142-0.32830.1125-0.0776-0.18380.19160.30460.0330.15340.04150.03150.17880.02050.239918.38779.1324-13.4124
35.57531.9756-1.78384.0387-1.07553.93050.1432-0.19390.1640.2071-0.18840.5030.1316-0.20160.04520.4399-0.0644-0.02630.0605-0.0390.101617.257426.48051.1837
42.33160.3628-0.05214.4056-1.80262.22650.19740.0197-0.4709-0.0538-0.2496-0.21970.18430.34520.05220.21520.0447-0.11040.1496-0.01810.171542.367929.779350.6095
56.03111.16523.79352.06521.12944.2978-0.03310.4893-0.212-0.12910.056-0.32170.05160.1953-0.02280.06020.05160.02050.1549-0.05660.304314.40088.793837.3345
66.20392.8609-0.60894.0670.18212.37860.0841-0.40020.4279-0.2435-0.25780.6288-0.1271-0.29950.17370.16280.0572-0.17620.0906-0.10560.242315.843326.329751.9591
72.3655-0.26440.40934.09841.81062.17080.06020.0432-0.5378-0.0129-0.09220.37760.5188-0.38510.0320.4518-0.1426-0.04970.14540.02370.179615.5602114.974224.065
84.8632-1.74682.43474.8569-0.7016.2013-0.1184-0.6132-0.4490.44050.01180.50270.2255-0.0060.10670.4512-0.1063-0.06720.20620.09420.36841.326594.018137.0001
96.3297-3.2415-1.50155.25490.81772.60030.15120.25850.09040.1769-0.1612-0.23660.12580.16590.010.3802-0.0339-0.11470.04310.02650.046242.3859111.439222.8191
102.17670.4065-0.03694.96762.45512.9368-0.1293-0.07070.52460.2123-0.21730.7132-0.0317-0.470.34670.345-0.01090.0120.2138-0.09570.341514.182554.3125.4459
115.7831.5916-2.08984.0457-1.45695.9335-0.09580.77040.4877-1.23260.12240.2037-0.6283-0.0218-0.02661.0342-0.03260.03850.12660.05820.229239.76275.407512.2931
125.72242.33571.56616.44022.30923.86530.1224-0.0634-0.1247-0.3890.0743-0.3898-0.02930.1879-0.19670.25050.01290.08870.0146-0.00270.045340.900658.04326.653
131.4116-0.805-0.33636.2641.92312.2970.0005-0.08270.22410.1461-0.52971.49050.0041-0.55610.52920.0541-0.0051-0.0110.2802-0.29810.624613.685753.809176.2979
145.73761.9232-3.34034.6134-1.16076.372-0.03290.5840.5689-0.92040.0730.3655-0.5015-0.1228-0.04010.3907-0.0058-0.1660.1320.0290.198638.481875.497562.0157
155.40032.63311.55196.02712.37262.69580.021-0.1618-0.1955-0.2299-0.086-0.25090.01230.07290.0650.09930.0182-0.01310.01540.01430.040340.56158.112976.1442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 10
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99
9X-RAY DIFFRACTION7G1 - 180
10X-RAY DIFFRACTION7I1 - 10
11X-RAY DIFFRACTION8G181 - 276
12X-RAY DIFFRACTION9H0 - 99
13X-RAY DIFFRACTION10J1 - 180
14X-RAY DIFFRACTION10L1 - 10
15X-RAY DIFFRACTION11J181 - 276
16X-RAY DIFFRACTION12K0 - 99
17X-RAY DIFFRACTION13M1 - 180
18X-RAY DIFFRACTION13O1 - 10
19X-RAY DIFFRACTION14M181 - 276
20X-RAY DIFFRACTION15N0 - 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