[English] 日本語
Yorodumi
- PDB-8cme: Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cme
TitleHuman Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Membrane peptide M176-190
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
  • Membrane protein
KeywordsIMMUNE SYSTEM / HLA-II / HLA-DR / HLA-DR1 / human leukocyte antigen / major histocompatibility complex / major histocompatibility complex class 2 / SARS-CoV-2 / coronavirus / COVID-19 / Membrane
Function / homology
Function and homology information


Maturation of protein M / SARS-CoV-2 modulates autophagy / cytoplasmic capsid assembly / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...Maturation of protein M / SARS-CoV-2 modulates autophagy / cytoplasmic capsid assembly / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / polysaccharide binding / host cell Golgi membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / CD28 dependent PI3K/Akt signaling / Generation of second messenger molecules / immunological synapse / endoplasmic reticulum-Golgi intermediate compartment / PD-1 signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / MHC class II antigen presentation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / T cell receptor binding / protein sequestering activity / trans-Golgi network membrane / VEGFR2 mediated vascular permeability / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Downstream TCR signaling / PIP3 activates AKT signaling / MHC class II protein complex binding / late endosome membrane / TRAF3-dependent IRF activation pathway / early endosome membrane / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Attachment and Entry / adaptive immune response / lysosome / immune response / lysosomal membrane / Golgi membrane / viral envelope / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / cell surface / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / 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 / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site ...M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / 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 / 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
HLA class II histocompatibility antigen, DR alpha chain / Membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsMacLachlan, B.J. / Mason, G.H. / Sourfield, D.O. / Godkin, A.J. / Rizkallah, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: Cell Rep / Year: 2023
Title: Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Authors: Chen, Y. / Mason, G.H. / Scourfield, D.O. / Greenshields-Watson, A. / Haigh, T.A. / Sewell, A.K. / Long, H.M. / Gallimore, A.M. / Rizkallah, P. / MacLachlan, B.J. / Godkin, A.
History
DepositionFeb 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: Membrane protein
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: Membrane protein
G: HLA class II histocompatibility antigen, DR alpha chain
H: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
I: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,53212
Polymers136,2129
Non-polymers3193
Water1,60389
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
C: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6615
Polymers45,4043
Non-polymers2572
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
F: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4664
Polymers45,4043
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: HLA class II histocompatibility antigen, DR alpha chain
H: Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)
I: Membrane protein


Theoretical massNumber of molelcules
Total (without water)45,4043
Polymers45,4043
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.374, 156.766, 165.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-102-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 45 or resid 48...
d_2ens_1(chain "D" and (resid 5 through 45 or resid 48...
d_3ens_1(chain "G" and (resid 5 through 45 or resid 48...
d_1ens_2(chain "B" and (resid 1 through 22 or resid 24...
d_2ens_2(chain "E" and (resid 1 through 22 or resid 24...
d_3ens_2(chain "H" and (resid 1 through 22 or resid 24...
d_1ens_3(chain "C" and (resid 1 through 10 or resid 12 through 14))
d_2ens_3(chain "F" and (resid 1 through 10 or resid 12 through 14))
d_3ens_3(chain "I" and (resid 1 through 10 or resid 12 through 14))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1HISHISLEULEUAA5 - 456 - 46
d_12ens_1PHEPHEGLYGLYAA48 - 4949 - 50
d_13ens_1PHEPHETHRTHRAA51 - 9352 - 94
d_14ens_1SERSERLEULEUAA95 - 9996 - 100
d_15ens_1PROPROCYSCYSAA102 - 107103 - 108
d_16ens_1ILEILEGLYGLYAA109 - 125110 - 126
d_17ens_1PROPROASPASPAA127 - 181128 - 182
d_21ens_1HISHISLEULEUDD5 - 456 - 46
d_22ens_1PHEPHEGLYGLYDD48 - 4949 - 50
d_23ens_1PHEPHETHRTHRDD51 - 9352 - 94
d_24ens_1SERSERLEULEUDD95 - 9996 - 100
d_25ens_1PROPROCYSCYSDD102 - 107103 - 108
d_26ens_1ILEILEGLYGLYDD109 - 125110 - 126
d_27ens_1PROPROASPASPDD127 - 181128 - 182
d_31ens_1HISHISLEULEUGG5 - 456 - 46
d_32ens_1PHEPHEGLYGLYGG48 - 4949 - 50
d_33ens_1PHEPHETHRTHRGG51 - 9352 - 94
d_34ens_1SERSERLEULEUGG95 - 9996 - 100
d_35ens_1PROPROCYSCYSGG102 - 107103 - 108
d_36ens_1ILEILEGLYGLYGG109 - 125110 - 126
d_37ens_1PROPROASPASPGG127 - 181128 - 182
d_11ens_2GLYGLYGLUGLUBB1 - 225 - 26
d_12ens_2VALVALGLNGLNBB24 - 3428 - 38
d_13ens_2GLUGLUTHRTHRBB36 - 5140 - 55
d_14ens_2LEULEUGLNGLNBB53 - 6457 - 68
d_15ens_2ASPASPVALVALBB66 - 9170 - 95
d_16ens_2ARGARGPROPROBB93 - 9797 - 101
d_17ens_2VALVALTHRTHRBB99 - 106103 - 110
d_18ens_2PROPROGLNGLNBB108 - 110112 - 114
d_19ens_2HISHISILEILEBB112 - 127116 - 131
d_110ens_2VALVALGLUGLUBB129 - 137133 - 141
d_111ens_2LYSLYSPROPROBB139 - 165143 - 169
d_112ens_2SERSERCYSCYSBB167 - 173171 - 177
d_113ens_2VALVALTRPTRPBB175 - 188179 - 192
d_114ens_2ALAALAALAALABB190194
d_21ens_2GLYGLYGLUGLUEE1 - 225 - 26
d_22ens_2VALVALGLNGLNEE24 - 3428 - 38
d_23ens_2GLUGLUTHRTHREE36 - 5140 - 55
d_24ens_2LEULEUGLNGLNEE53 - 6457 - 68
d_25ens_2ASPASPVALVALEE66 - 9170 - 95
d_26ens_2ARGARGPROPROEE93 - 9797 - 101
d_27ens_2VALVALTHRTHREE99 - 106103 - 110
d_28ens_2PROPROGLNGLNEE108 - 110112 - 114
d_29ens_2HISHISILEILEEE112 - 127116 - 131
d_210ens_2VALVALGLUGLUEE129 - 137133 - 141
d_211ens_2LYSLYSPROPROEE139 - 165143 - 169
d_212ens_2SERSERCYSCYSEE167 - 173171 - 177
d_213ens_2VALVALTRPTRPEE175 - 188179 - 192
d_214ens_2ALAALAALAALAEE190194
d_31ens_2GLYGLYGLUGLUHH1 - 225 - 26
d_32ens_2VALVALGLNGLNHH24 - 3428 - 38
d_33ens_2GLUGLUTHRTHRHH36 - 5140 - 55
d_34ens_2LEULEUGLNGLNHH53 - 6457 - 68
d_35ens_2ASPASPVALVALHH66 - 9170 - 95
d_36ens_2ARGARGPROPROHH93 - 9797 - 101
d_37ens_2VALVALTHRTHRHH99 - 106103 - 110
d_38ens_2PROPROGLNGLNHH108 - 110112 - 114
d_39ens_2HISHISILEILEHH112 - 127116 - 131
d_310ens_2VALVALGLUGLUHH129 - 137133 - 141
d_311ens_2LYSLYSPROPROHH139 - 165143 - 169
d_312ens_2SERSERCYSCYSHH167 - 173171 - 177
d_313ens_2VALVALTRPTRPHH175 - 188179 - 192
d_314ens_2ALAALAALAALAHH190194
d_11ens_3LEULEUGLNGLNCC1 - 101 - 10
d_12ens_3VALVALGLYGLYCC12 - 1412 - 14
d_21ens_3LEULEUGLNGLNFF1 - 101 - 10
d_22ens_3VALVALGLYGLYFF12 - 1412 - 14
d_31ens_3LEULEUGLNGLNII1 - 101 - 10
d_32ens_3VALVALGLYGLYII12 - 1412 - 14

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.317943607386, 0.945634108962, 0.0684689308394), (0.94444596027, 0.322230546086, -0.0647248275238), (-0.0832687855775, 0.044086359985, -0.995551456335)-34.4544032584, -34.9627124547, -52.1702946145
2given(0.783358103363, 0.610344023449, -0.117602104299), (0.602032957475, -0.792095169526, -0.100705315294), (-0.154616946061, 0.00808798213105, -0.987941387197)-23.9421762677, 64.832292334, -18.1929277992
3given(-0.328394366062, 0.941684891305, 0.0733941811558), (0.941349533047, 0.332677279573, -0.0564524958448), (-0.0775770389369, 0.0505508965738, -0.995703977036)-33.2292163377, -35.2377881116, -53.260593559
4given(0.792407618497, 0.601480038179, -0.101547672652), (0.595566340146, -0.79886232317, -0.0843784516616), (-0.131874564014, 0.00638375218218, -0.991245856019)-23.4407666848, 66.3058770428, -20.0366696078
5given(-0.314227441516, 0.948668706044, 0.035899877036), (0.938308271519, 0.316101448679, -0.140205070318), (-0.144356165778, -0.0103711289642, -0.98947144329)-36.0155047134, -36.3381301502, -43.4590127076
6given(0.78120004246, 0.594854987693, -0.189404427816), (0.592040685374, -0.802174764325, -0.0774820904524), (-0.198026060208, -0.0516061149061, -0.978837314564)-24.9347175252, 67.0645197239, -10.2431221807

-
Components

-
Protein , 2 types, 6 molecules ADGBEH

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21287.102 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01903
#2: Protein Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)


Mass: 22487.186 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Protein/peptide , 1 types, 3 molecules CFI

#3: Protein/peptide Membrane protein / / M / E1 glycoprotein / Matrix glycoprotein / Membrane glycoprotein


Mass: 1629.814 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC5

-
Non-polymers , 3 types, 92 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M MES pH 5.0, 20 % PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→47.29 Å / Num. obs: 69030 / % possible obs: 99.81 % / Redundancy: 13.7 % / Biso Wilson estimate: 62.91 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0996 / Rpim(I) all: 0.0279 / Rrim(I) all: 0.104 / Net I/σ(I): 16.05
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 3.099 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6779 / CC1/2: 0.378 / CC star: 0.741 / Rpim(I) all: 0.867 / Rrim(I) all: 3.219 / % possible all: 98.96

-
Processing

Software
NameVersionClassification
DIALSdata scaling
DIALSdata reduction
PHASERphasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→47.28 Å / SU ML: 0.4203 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2401 3407 4.94 %
Rwork0.198 65570 -
obs0.2001 68977 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.35 Å2
Refinement stepCycle: LAST / Resolution: 2.26→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9520 0 20 89 9629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00469827
X-RAY DIFFRACTIONf_angle_d0.788113365
X-RAY DIFFRACTIONf_chiral_restr0.05121424
X-RAY DIFFRACTIONf_plane_restr0.00691753
X-RAY DIFFRACTIONf_dihedral_angle_d13.5033613
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.693843788776
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.554098522297
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.796877590522
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.934620605633
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.631271181572
ens_3d_3CX-RAY DIFFRACTIONTorsion NCS0.71170316758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.43791180.41412606X-RAY DIFFRACTION96.66
2.29-2.330.40051460.37662707X-RAY DIFFRACTION99.79
2.33-2.360.36331490.34612743X-RAY DIFFRACTION99.86
2.36-2.40.3591400.33712689X-RAY DIFFRACTION99.82
2.4-2.440.28881320.30482690X-RAY DIFFRACTION99.89
2.44-2.490.3581500.29042712X-RAY DIFFRACTION99.93
2.49-2.530.31271360.28452714X-RAY DIFFRACTION99.89
2.53-2.590.29991270.27442714X-RAY DIFFRACTION99.89
2.59-2.640.33051440.28452698X-RAY DIFFRACTION99.96
2.64-2.70.30621360.28452746X-RAY DIFFRACTION99.97
2.7-2.770.33491360.28562732X-RAY DIFFRACTION99.97
2.77-2.850.31091360.28112746X-RAY DIFFRACTION99.97
2.85-2.930.31531550.26762702X-RAY DIFFRACTION99.93
2.93-3.020.34351480.26912714X-RAY DIFFRACTION100
3.02-3.130.30571500.26032718X-RAY DIFFRACTION99.93
3.13-3.260.28581350.23442730X-RAY DIFFRACTION100
3.26-3.410.26251670.24232712X-RAY DIFFRACTION100
3.41-3.590.27441510.21072746X-RAY DIFFRACTION100
3.59-3.810.21831380.18732734X-RAY DIFFRACTION100
3.81-4.10.21131290.17742765X-RAY DIFFRACTION100
4.1-4.520.18261490.14052758X-RAY DIFFRACTION100
4.52-5.170.17591370.13332801X-RAY DIFFRACTION100
5.17-6.510.19051460.15622806X-RAY DIFFRACTION100
6.51-47.280.2021520.15172887X-RAY DIFFRACTION99.28
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)
17.86941576419-5.28737029968-3.699738056243.895169320013.613647157916.75765076048-0.497395713198-0.365367586958-0.1448773007180.8756206916160.1883606558320.1486387563280.565756435292-0.05434309960230.2592546731430.679612134772-0.1077456573650.01168720630210.3863032862280.1016421281930.4518926042467.557163746275.4440980207-23.2317818058
24.5011883231-1.702389916550.3059812573864.79815956844-0.5879009986992.461427189540.2356657170890.439023234224-0.0751318495056-0.69154773099-0.279855810059-0.3310820592820.1736165876240.2296266099610.03995055235530.537930723174-0.0366345878351-0.03175851988740.4584418920510.04966500362340.39515401602169.458256067969.8184253383-33.7467020529
36.825351427232.6025793818-0.2200078409291.725434087151.168329851682.09841547928-0.256727571455-0.4298647477540.3715020198570.0906603638129-0.03301751234150.609740342662-0.176917948585-0.2549621580340.3248134221140.626511979108-0.174683373969-0.09735109013010.5089895037290.08728372008110.59847016733242.81520198160.2552884867-22.7246938099
44.582143062280.473463130061-0.2111197805992.12218897841-0.4335212645960.0657472959145-0.02224637095110.2400119868910.0958843082066-0.220322628657-0.0313314134418-0.03815592362890.1285710316-0.09657080328720.004128079429320.613471142437-0.102156369745-0.07361993545720.513174941610.1078273340810.45915265069356.028224705259.6817788937-28.0637924536
57.386684167571.27174760355-0.9196420647631.43468439656-0.4383079606391.995367717730.226448788914-0.348397871409-1.2867919276-0.306524226052-0.1421054307920.02049816754190.522135244141-0.188835796215-0.09081627194430.710913939399-0.112454000614-0.1373451096410.4913897916360.1231025910640.60014328066950.385552209450.3479663206-24.9273789037
62.95985044983-1.74032299321-1.38764909015.286097102881.744216704453.312454839570.0785774949932-0.09038651084020.0324603443980.109999241114-0.347975245629-0.6737903985150.05177484174550.3875057880020.2651405458490.522382968138-0.0628484879687-0.1186430343670.5937878219660.1380742341160.56070054115679.291912562173.1342774664-22.9272035899
75.357123431061.62213909264-1.027215145112.89476281203-1.28886565761.854586853450.1347615433780.3060368743240.09828725499650.2859966139680.0113249403964-0.0682568643571-0.144579986944-0.163626970191-0.1588212399350.532290039757-0.058596214235-0.1339500258040.36848782338-0.06498872902310.30861953870656.867940600677.9434883676-20.179499763
86.66166000731.49121609813-3.771221011052.9979321756-2.710748303315.768251605890.34903710361-0.4563190190420.1218709246680.3809497996270.03719085180330.458871908278-0.400058365249-0.143450548527-0.357633928160.510200572145-0.100998338503-0.07478560156030.4785254501740.05064523922280.54552166951440.695748952770.5842982831-8.14359535753
95.22294877498-5.322050585446.644436666375.68598161866-7.173997810668.063027737071.173998608372.81100671701-0.311280363522-1.28732781791-1.42155194492-0.2963668619720.1401457598880.842956030173-0.096473849730.604490192114-0.05793812236810.01792649960760.578475560697-0.02904814625080.65266793661476.24042330478.9911944097-34.7843602942
100.1065030705540.524715270427-0.3183566494271.086826718980.0640317567392-0.132548033851-0.12033158607-0.0384272184210.125029107369-0.3029620892670.1497428954690.236762569053-0.2752232716560.0908829306367-0.01197545734280.64702471986-0.165772242399-0.2389208488960.6170735007850.1336913442440.7737112699819.5463594476854.8022266707-26.7164201157
114.62441480009-1.7077205853-5.088246080716.926794821452.881498651975.85493613016-0.207360214448-0.4628975862970.01500430891590.3330834629240.225838721344-0.1131729509760.3366828882820.0560493881522-0.01809434817480.591601476524-0.113970394606-0.2352193058420.5896145384020.146643315920.52173482597316.513970242148.6090144813-17.9347853979
121.605532671751.185998344250.3236880803576.237212660140.7703174720941.73309698014-0.1460975033420.04831609864860.619168312602-0.288507766991-0.006540487163220.890072233351-0.426500157476-0.2167897175190.04889350988140.518626274121-0.077723607154-0.172812226620.5331757958190.1286578156220.6084934155531.303480306351.053905512-26.3248726771
131.987486992410.647630211820.9905672942175.282718701470.342505071261.13902093136-0.07000210126780.1082739548280.2914698325670.161496581378-0.1164201015050.116715386766-0.06800752547450.08830152479210.1584933383570.509871300267-0.121892411696-0.1385090564620.5646268693130.0864440411370.419251679669-0.18650783440235.8440230964-27.3613970569
146.999963528970.566558765188-1.829408886581.127600180430.2456797125441.81446872832-0.08394313535610.4635452314340.581288218682-0.3811297430060.08121750555980.50397927805-0.130361546888-0.114818507272-0.0405176894680.779533345068-0.15360150696-0.2994146363280.6384768065220.2692334757370.8234853230428.2325733663959.0700644805-31.278727629
153.017763023612.89332129855-1.937757222645.16077387619-2.930263787224.05590807729-0.4117566437420.6828564202430.861482087405-0.6338960061540.4599932108570.8289044700560.261918771117-0.489983680317-0.09761088479870.913418552136-0.21985536879-0.4191408292380.8039982027080.4216153122181.023527389528.3300905552867.8343114776-36.5956243797
163.612917278293.86021682681-3.243523238757.69848777421-2.245436374963.485601800420.222559893113-0.04329152154911.424944081660.0385980502231-0.1660644947581.81386814145-0.890519811056-0.801785951163-0.4521760846110.9265770715920.00346845897039-0.2047685577750.8424548138720.3904672710391.604455347434.0533074984675.3566938832-32.3550266135
172.76539268198-3.81276959328-0.1466422821786.96750463026-1.02867279291.24480479961-0.173677064679-0.2322908346480.9521132824280.6806702594310.358230613238-0.32689917269-0.6967409309450.0817092471526-0.1198646538620.859661107711-0.254735546722-0.2175879481130.682000987090.1862465705881.0506027963219.389660551472.0128529626-28.4392214561
181.357304116610.6610718296821.296531342096.232731983993.539081264162.36015281212-0.1096932811180.296821580621-0.0551510261883-0.124928069550.27980464639-0.0623034397705-0.05143843517720.285774260389-0.2252136166420.53092781543-0.157495584452-0.1145469645710.5804815600650.1819617931150.47094717662919.027520189532.5052805892-37.1331499539
192.97906836985-1.85405563126-1.690765399354.881738334615.475468303095.188760565880.7613781172340.373196836129-0.0244713950563-0.413694803806-0.273121676576-0.969283836575-0.5628161547160.664204838038-0.5150191850360.6226051823-0.107987032013-0.06613196263080.8920725669230.05210105603570.67822662363221.792297619531.8314453503-45.1024362105
202.267766031770.6875959332741.006822346743.410044486972.995174235184.934740709910.09887405863880.035395027583-0.120230368172-0.287025835435-0.406104893792-0.0376443028304-0.3541945845160.111012465590.1715317767750.577671352967-0.0601197296111-0.1399354531020.6687591042210.09493070153990.52363960093815.415603354730.6786204122-44.2462006537
216.67792009221.207227882812.835365518063.810279497985.417164712892.672537079050.1606955386720.446635722672-0.40814341032-0.8899307997740.388097358885-0.9827428082-0.3772246411751.02911755348-0.5916231582460.604545484569-0.06454091291-0.04500260509170.6238851927590.00726925153930.59188011158624.075552837122.5021088203-45.6086211837
223.82203002331.135806561490.2421636170161.999842128931.796011541663.653006889410.111866340192-0.6646980764110.267432604720.762558885285-0.05039782656570.800034639307-0.243703058738-0.06357794112060.07070491203980.814362998969-0.330138566181-0.1046188311970.7437344515390.05615692180190.87796087457414.052961537364.9249981395-20.7409475793
236.13417228403-1.889549081990.1681548234985.22853930609-1.246693264391.59481099102-0.03373378963380.509338424256-0.00934414363312-0.3978927275740.477802911436-0.5884368200450.3871089108360.458163207668-0.2844672017650.4891241115690.02714444914130.07797646541260.5444705288050.1655438577680.52268805791878.248907659348.4180989586-5.62639439358
242.139002503812.519214999770.1214563499269.264621941041.101220633590.229653255913-0.0556515025621-0.2477267245980.009149947305290.2637540123250.1393917554120.771598172236-0.1227478544720.0158095712843-0.1329321536230.5879686844460.06038616448260.02142783212920.6418126850670.1333077419120.53228528453874.011198473950.50502881016.60846825852
259.075225062875.59021585837-0.3699133068613.91221232721-1.908972906264.15811226705-0.137958864175-0.553438241864-0.1080249412810.8925435923890.352295669990.207358223883-0.472543437979-0.736996513587-0.3996110705730.7474014852780.1953480823270.05755041313150.7738439464780.2188680556960.52001606914174.473234080237.60331426329.42061362725
267.964711628160.819651430121.852819985795.91598803195-0.2757918897313.44183691981-0.0754742872244-0.3787790501760.8945809251610.205201943484-0.0519913457307-0.749357695971-0.2015782978740.2700927907780.1453405832910.38662063010.0542380850670.07951363210180.4723583047130.02006708965340.47214834071281.145618498565.4765989281.60379241174
275.948685562520.0319589294091-0.302836912530.3494436519220.321064539191.611122511660.141728705779-0.585793127645-0.56901575-0.00196103270359-0.0905850548979-0.01457742918930.502233346901-0.220393255707-0.04919534942090.54142541636-0.0330173518094-0.07455748699860.5880749383630.2085006977970.544135136657.719114397652.40481190860.528082804289
283.889282074634.64482566777-0.9419138330649.287924374070.04133417105841.903996185920.172814104593-0.6134689422580.479144956677-0.133582848649-0.2242891307181.0569045535-0.0183804221147-0.3572907021140.02144061716890.4605604863230.0300052117969-0.04780570388640.5983375225310.1624588262810.64904804012449.027302363857.2835232571-0.701492260802
293.70150306401-2.59465246663-1.45117482613.006834260671.239386058192.58479888715-0.176226769444-0.220700919553-0.01326068083910.08952178712760.0883805587917-0.09256461962530.2884375715450.484633357360.196437227260.5404342086120.0229027673830.04438058321890.6448441305620.1670194736870.51084855992180.077410288354.6955529336-5.25353662249
304.42422967523-1.82616985801-0.5839434337322.51766254671.675362082181.234885029850.03217128350920.2844880565720.707570587449-0.4707807996160.0967746068657-0.559153398147-0.05622790523210.350685006828-0.07627008304710.6713252658940.03949672785820.1470133134510.6689067253290.2262301690020.74010154522390.849898242759.6168523015-9.63499311682
313.49325212160.6040015177350.7693448415911.98231137068-0.747950970861.950024827540.280687268309-0.369997856738-0.532975696704-0.218729966535-0.0818742989913-0.2226076150050.381903034726-0.0319822711687-0.2521970462420.6410502192040.08516081275320.07452561046540.4443382217420.03474971138330.49772529588471.184116155239.4058363535-6.67286995986
324.57461988549-1.458419919573.651238312242.61319409523-1.73770770815.377463295910.3716868783110.0659497526336-0.960129505558-0.4416067799350.07366577927210.3428330704590.933292609789-0.112345499102-0.4566512330890.629964159154-0.0914084283922-0.07125028252470.5969954823090.1538632976530.75385688316852.620502835135.1157098761-16.7398358043
338.686888809278.11707747301-1.109572890288.238019260560.567905886534.639381509450.0744256809809-0.3398696126920.376475850850.9091927341130.3219703258690.2454541115410.0005767588046780.274345527221-0.3666572106010.5973223733770.183440396012-0.005570437172860.8088825665820.1092964263680.68739727602588.095250651151.57550843394.20423931904
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 14 )AA1 - 141 - 14
22chain 'A' and (resid 15 through 87 )AA15 - 8715 - 87
33chain 'A' and (resid 88 through 101 )AA88 - 10188 - 101
44chain 'A' and (resid 102 through 154 )AA102 - 154102 - 154
55chain 'A' and (resid 155 through 182 )AA155 - 182155 - 182
66chain 'B' and (resid 0 through 64 )BB0 - 641 - 65
77chain 'B' and (resid 65 through 111 )BB65 - 11166 - 112
88chain 'B' and (resid 112 through 190 )BB112 - 190113 - 191
99chain 'C' and (resid 1 through 15 )CC1 - 151 - 15
1010chain 'D' and (resid 2 through 26 )DD2 - 261 - 25
1111chain 'D' and (resid 27 through 55 )DD27 - 5526 - 54
1212chain 'D' and (resid 56 through 101 )DD56 - 10155 - 100
1313chain 'D' and (resid 102 through 182 )DD102 - 182101 - 181
1414chain 'E' and (resid 0 through 32 )EE0 - 321 - 33
1515chain 'E' and (resid 33 through 51 )EE33 - 5134 - 52
1616chain 'E' and (resid 52 through 62 )EE52 - 6253 - 63
1717chain 'E' and (resid 63 through 78 )EE63 - 7864 - 79
1818chain 'E' and (resid 79 through 122 )EE79 - 12280 - 123
1919chain 'E' and (resid 123 through 133 )EE123 - 133124 - 134
2020chain 'E' and (resid 134 through 164 )EE134 - 164135 - 165
2121chain 'E' and (resid 165 through 190 )EE165 - 190166 - 191
2222chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
2323chain 'G' and (resid 1 through 14 )GG1 - 141 - 14
2424chain 'G' and (resid 15 through 45 )GG15 - 4515 - 45
2525chain 'G' and (resid 46 through 55 )GG46 - 5546 - 55
2626chain 'G' and (resid 56 through 87 )GG56 - 8756 - 87
2727chain 'G' and (resid 88 through 153 )GG88 - 15388 - 153
2828chain 'G' and (resid 154 through 182 )GG154 - 182154 - 182
2929chain 'H' and (resid 0 through 32 )HH0 - 321 - 33
3030chain 'H' and (resid 33 through 64 )HH33 - 6434 - 65
3131chain 'H' and (resid 65 through 111 )HH65 - 11166 - 112
3232chain 'H' and (resid 112 through 190 )HH112 - 190113 - 191
3333chain 'I' and (resid 1 through 15 )II1 - 151 - 15

+
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