[English] 日本語
Yorodumi
- PDB-6rp9: Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rp9
TitleCrystal structure of the T-cell receptor NYE_S3 bound to HLA A2*01-SLLMWITQV
Components
  • Beta-2-microglobulin
  • Cancer/testis antigen 1
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • T-cell receptor alpha chain
  • T-cell receptor beta chain
KeywordsIMMUNE SYSTEM / T-cell receptor / peptide-Human leukocyte antigen complex / NY-ESO-1 / cancer testis antigen
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...tRNA threonylcarbamoyladenosine metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / 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 / 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 / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / 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 / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / 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 / : ...CTAG/Pcc1 family / Transcription factor Pcc1 / 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, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Cancer/testis antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsColes, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. ...Coles, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Vuidepot, A. / Jakobsen, B.K. / Harper, S.
CitationJournal: J Immunol. / Year: 2020
Title: TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex.
Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / ...Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / Chester, F. / Wiederhold, K. / Robinson, R.A. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Jakobsen, B.K. / Vuidepot, A. / Harper, S.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.4Oct 23, 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-2 alpha chain
B: Beta-2-microglobulin
C: Cancer/testis antigen 1
D: T-cell receptor alpha chain
E: T-cell receptor beta chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Cancer/testis antigen 1
I: T-cell receptor alpha chain
J: T-cell receptor beta chain
K: T-cell receptor alpha chain
L: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)241,50112
Polymers241,50112
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Cancer/testis antigen 1
D: T-cell receptor alpha chain
E: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,5185
Polymers95,5185
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Cancer/testis antigen 1
I: T-cell receptor alpha chain
J: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,5185
Polymers95,5185
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: T-cell receptor alpha chain
L: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)50,4662
Polymers50,4662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.570, 85.610, 171.920
Angle α, β, γ (deg.)90.00, 91.78, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14D
24K
15E
25J
16E
26L
17I
27K
18J
28L
19J
29L
110E
210L
111I
211K
112D
212I
113D
213K
114E
214J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 275
2114F1 - 275
1124B0 - 99
2124G0 - 99
1134D3 - 107
2134I3 - 107
1144D7 - 107
2144K7 - 107
1154E1 - 64
2154J1 - 64
1164E2 - 64
2164L2 - 64
1174I7 - 107
2174K7 - 107
1184J2 - 64
2184L2 - 64
1194J72 - 243
2194L72 - 243
11104E72 - 243
21104L72 - 243
11114I116 - 199
21114K116 - 199
11124D116 - 198
21124I116 - 198
11134D116 - 199
21134K116 - 199
11144E72 - 244
21144J72 - 244

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.735114, -0.032576, -0.677161), (-0.013889, 0.999359, -0.032998), (0.677801, -0.014852, -0.735095)50.02382, -4.26145, 85.59537
3given(1), (1), (1)
4given(-0.733984, -0.027087, -0.678626), (-0.005665, 0.999414, -0.033764), (0.679143, -0.020938, -0.733707)50.07603, -4.31286, 85.45335
5given(1), (1), (1)
6given(-0.73471, 0.056708, -0.676007), (0.020196, 0.997887, 0.061759), (0.67808, 0.031722, -0.734303)48.8544, -3.78238, 85.10164
7given(1), (1), (1)
8given(-0.547093, -0.273854, -0.791008), (-0.293396, -0.822288, 0.487607), (-0.78397, 0.498845, 0.36952)124.72198, 31.80466, -1.35619
9given(1), (1), (1)
10given(-0.734919, 0.047543, -0.676487), (0.017259, 0.998528, 0.051426), (0.677936, 0.026119, -0.734657)49.07241, -3.868, 85.18219
11given(1), (1), (1)
12given(-0.635231, -0.214844, -0.741838), (-0.30472, -0.812885, 0.49635), (-0.709667, 0.54135, 0.450902)115.17016, 30.41178, -6.18807
13given(1), (1), (1)
14given(-0.135136, 0.523322, 0.841352), (-0.349182, -0.819817, 0.453842), (0.92726, -0.232454, 0.293522)-113.643, 37.00259, 14.42074
15given(1), (1), (1)
16given(-0.019482, 0.510732, 0.859519), (-0.352954, -0.807845, 0.472027), (0.935438, -0.294175, 0.196003)-109.92369, 34.99571, 24.17966
17given(1), (1), (1)
18given(-0.031233, 0.504808, 0.862667), (-0.315026, -0.82407, 0.470816), (0.948569, -0.257057, 0.184766)-109.94206, 36.80414, 22.68023
19given(1), (1), (1)
20given(-0.638274, -0.230168, -0.734595), (-0.261097, -0.832965, 0.487851), (-0.724179, 0.503183, 0.471563)115.71024, 32.96675, -5.06232
21given(1), (1), (1)
22given(-0.062031, 0.505789, 0.860424), (-0.300223, -0.831614, 0.46721), (0.95185, -0.229338, 0.203436)-111.33941, 38.0867, 20.77706
23given(1), (1), (1)
24given(-0.73119, 0.044299, -0.680734), (0.01063, 0.998508, 0.053561), (0.682091, 0.031927, -0.73057)49.27967, -4.10373, 85.34093
25given(1), (1), (1)
26given(-0.615625, -0.250692, -0.7471), (-0.250283, -0.836764, 0.487016), (-0.747238, 0.486806, 0.452389)118.25117, 33.78144, -4.55277
27given(1), (1), (1)
28given(-0.729908, 0.044849, -0.682072), (0.008422, 0.99836, 0.056633), (0.683493, 0.035593, -0.729088)49.27406, -4.12585, 85.30721

-
Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 32082.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
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
#3: Protein/peptide Cancer/testis antigen 1 / Autoimmunogenic cancer/testis antigen NY-ESO-1 / Cancer/testis antigen 6.1 / CT6.1 / L antigen ...Autoimmunogenic cancer/testis antigen NY-ESO-1 / Cancer/testis antigen 6.1 / CT6.1 / L antigen family member 2 / LAGE-2


Mass: 1090.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78358
#4: Protein T-cell receptor alpha chain


Mass: 22844.078 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T-cell receptor beta chain


Mass: 27621.572 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulphate, 15 % PEG8k, 0.1 M Tris pH7.5

-
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-F / Detector: PIXEL / Date: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.12→85.61 Å / Num. obs: 52792 / % possible obs: 100 % / Redundancy: 6.76 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.047 / Net I/σ(I): 10.99
Reflection shellResolution: 3.12→3.2 Å / Redundancy: 3.97 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 2717 / CC1/2: 0.627 / Rpim(I) all: 0.567 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia20.5.436-g557f8872-dials-1.7data reduction
xia20.5.436-g557f8872-dials-1.7data scaling
PHASERVersion 2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E)

5e00

3qdj

5d2n


Resolution: 3.12→68.01 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 62.726 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25046 2717 4.9 %RANDOM
Rwork0.22349 ---
obs0.22481 52792 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.682 Å2
Baniso -1Baniso -2Baniso -3
1--3.55 Å2-0 Å2-2.27 Å2
2---1.37 Å2-0 Å2
3---5.05 Å2
Refinement stepCycle: LAST / Resolution: 3.12→68.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16633 0 0 0 16633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01917088
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214837
X-RAY DIFFRACTIONr_angle_refined_deg0.9291.92923203
X-RAY DIFFRACTIONr_angle_other_deg0.796334509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95352068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05723.763877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.213152718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.83915128
X-RAY DIFFRACTIONr_chiral_restr0.060.22423
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02119251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023737
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6296.4288309
X-RAY DIFFRACTIONr_mcbond_other0.6296.4288308
X-RAY DIFFRACTIONr_mcangle_it1.1669.64110364
X-RAY DIFFRACTIONr_mcangle_other1.1669.64110365
X-RAY DIFFRACTIONr_scbond_it0.4186.4328779
X-RAY DIFFRACTIONr_scbond_other0.4186.4328780
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7929.63112840
X-RAY DIFFRACTIONr_long_range_B_refined1.85971.0517663
X-RAY DIFFRACTIONr_long_range_B_other1.85971.05117664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
114240medium positional0.180.5
221600medium positional0.130.5
331309medium positional0.10.5
441249medium positional0.240.5
55807medium positional0.120.5
66798medium positional0.290.5
771249medium positional0.240.5
88798medium positional0.290.5
992566medium positional0.20.5
10102566medium positional0.230.5
11111141medium positional0.230.5
12121219medium positional0.190.5
13131141medium positional0.260.5
14142582medium positional0.160.5
114240medium thermal2.822
221600medium thermal3.262
331309medium thermal2.42
441249medium thermal3.042
55807medium thermal3.62
66798medium thermal2.932
771249medium thermal3.062
88798medium thermal1.622
992566medium thermal2.82
10102566medium thermal3.142
11111141medium thermal2.372
12121219medium thermal3.132
13131141medium thermal4.642
14142582medium thermal2.032
LS refinement shellResolution: 3.12→3.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 193 -
Rwork0.369 3877 -
obs--99.83 %
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)
16.33131.22770.61931.9734-0.52192.93350.2076-0.1640.58940.0656-0.02670.5545-0.4076-0.2849-0.18090.08110.01020.02960.1379-0.02560.42835.13833.048271.5446
25.65112.42571.29714.29140.21566.01260.03820.4859-0.4404-0.4332-0.04260.25380.9649-0.36010.00440.2155-0.0481-0.09160.1178-0.04480.453730.7075-15.762370.3928
36.2096-0.09017.58485.46691.766723.240.4853-0.02240.2178-0.0296-0.4117-0.5303-0.6625-0.498-0.07360.2227-0.09780.02280.3048-0.02180.380154.53558.330973.6034
47.40330.2268-1.91962.2384-0.2892.38820.0840.3140.4789-0.24070.1042-0.7635-0.42140.3777-0.18820.2967-0.07810.05240.209-0.00790.617988.210732.202469.9875
55.21571.1644-0.46342.41230.62581.62270.1169-0.18340.3307-0.13760.0517-0.4773-0.0740.4019-0.16860.0364-0.0242-0.04230.1484-0.00260.574492.559713.285268.0313
63.3668-1.39470.83812.025-0.72951.6726-0.3256-0.7520.47320.44820.2701-0.4706-0.333-0.13860.05550.66370.1428-0.28931.1126-0.02030.65631.32187.997620.1681
74.0164-1.24540.44243.2117-0.43363.0343-0.486-1.0953-0.58170.74130.55090.37190.4334-0.2915-0.06490.79940.1444-0.24451.11550.25760.59034.0579-10.601724.5798
84.89292.1756-10.16380.9706-4.53421.2082-0.2686-0.059-0.1426-0.09010.0174-0.06960.5085-0.15910.25120.590.1204-0.17980.8520.06980.4516-11.694912.63835.3299
94.8534-0.99512.46372.0181-0.11252.0826-0.0773-0.37880.59860.0027-0.02490.4038-0.3375-0.25530.10230.74070.0003-0.18580.7763-0.00310.7603-38.561337.5194-13.427
103.3194-0.631.75431.3997-0.59492.6171-0.094-0.39990.03730.02770.00810.0855-0.029-0.14030.08590.5097-0.022-0.23430.6697-0.02080.4315-43.25318.7295-15.9459
113.37780.89582.38832.47610.71295.8646-0.0140.3147-0.2341-0.26050.22170.07310.5013-0.2221-0.20770.4698-0.0062-0.09420.2110.06480.6753-36.867645.159556.4771
123.27371.70021.74822.77590.47262.73090.11230.485-0.1868-0.57210.2452-0.250.25950.0218-0.35750.34010.0351-0.1010.3917-0.02080.5087-33.011958.450941.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D4 - 217
5X-RAY DIFFRACTION5E1 - 256
6X-RAY DIFFRACTION6F1 - 275
7X-RAY DIFFRACTION7G0 - 99
8X-RAY DIFFRACTION8H1 - 9
9X-RAY DIFFRACTION9I4 - 218
10X-RAY DIFFRACTION10J1 - 256
11X-RAY DIFFRACTION11K8 - 218
12X-RAY DIFFRACTION12L2 - 256

+
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