[English] 日本語
Yorodumi
- PDB-5jwe: Crystal structure of H-2Db in complex with the LCMV-derived GP92-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jwe
TitleCrystal structure of H-2Db in complex with the LCMV-derived GP92-101 peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsIMMUNE SYSTEM / Immunology / antigen presentation / MHC class I
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / receptor-mediated endocytosis of virus by host cell ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / receptor-mediated endocytosis of virus by host cell / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / host cell endoplasmic reticulum membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBuratto, J. / Badia-Martinez, D. / Norstrom, M. / Sandalova, T. / Achour, A.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structures of H-2Db in complex with the LCMV-derived peptides GP92 and GP392 explain pleiotropic effects of glycosylation on antigen presentation and immunogenicity.
Authors: Hafstrand, I. / Badia-Martinez, D. / Josey, B.J. / Norstrom, M. / Buratto, J. / Pellegrino, S. / Duru, A.D. / Sandalova, T. / Achour, A.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
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 1.2Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
P: Pre-glycoprotein polyprotein GP complex
Q: Pre-glycoprotein polyprotein GP complex
R: Pre-glycoprotein polyprotein GP complex
S: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,38740
Polymers179,75712
Non-polymers2,63028
Water4,918273
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
P: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59610
Polymers44,9393
Non-polymers6577
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-41 kcal/mol
Surface area18770 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
Q: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59210
Polymers44,9393
Non-polymers6537
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-42 kcal/mol
Surface area18900 Å2
MethodPISA
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
R: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4128
Polymers44,9393
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-57 kcal/mol
Surface area18520 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
S: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,78812
Polymers44,9393
Non-polymers8499
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-71 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.500, 176.300, 85.600
Angle α, β, γ (deg.)90.000, 119.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:6 or (resid 7 and (name...
21(chain C and (resseq 1:6 or (resid 7 and (name...
31(chain E and (resseq 1:6 or (resid 7 and (name...
41(chain G and (resseq 1:6 or (resid 7 and (name...
12(chain B and (resseq 2 or (resid 3 and (name...
22(chain D and (resseq 2:18 or resseq 20:33 or resseq...
32(chain F and (resseq 2 or (resid 3 and (name...
42(chain H and (resseq 2 or (resid 3 and (name...
13(chain Q and (resseq 1:8 or (resid 9 and (name...
23(chain P and (resseq 1:8 or (resid 9 and (name...
33(chain R and (resseq 1:8 or (resid 9 and (name...
43(chain S and (resseq 1:8 or (resid 9 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:6 or (resid 7 and (name...A0
211(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 6
221(chain C and (resseq 1:6 or (resid 7 and (name...C7
231(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
241(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
251(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
261(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
271(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
281(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
291(chain C and (resseq 1:6 or (resid 7 and (name...C1 - 276
311(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 6
321(chain E and (resseq 1:6 or (resid 7 and (name...E7
331(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
341(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
351(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
361(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
371(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
381(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
391(chain E and (resseq 1:6 or (resid 7 and (name...E1 - 276
411(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 6
421(chain G and (resseq 1:6 or (resid 7 and (name...G7
431(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
441(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
451(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
461(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
471(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
481(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
491(chain G and (resseq 1:6 or (resid 7 and (name...G1 - 276
112(chain B and (resseq 2 or (resid 3 and (name...B2
122(chain B and (resseq 2 or (resid 3 and (name...B3
132(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
142(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
152(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
162(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
172(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
182(chain B and (resseq 2 or (resid 3 and (name...B1 - 99
212(chain D and (resseq 2:18 or resseq 20:33 or resseq...D2 - 18
222(chain D and (resseq 2:18 or resseq 20:33 or resseq...D20 - 33
232(chain D and (resseq 2:18 or resseq 20:33 or resseq...D35
242(chain D and (resseq 2:18 or resseq 20:33 or resseq...D37 - 43
252(chain D and (resseq 2:18 or resseq 20:33 or resseq...D44
262(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
272(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
282(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
292(chain D and (resseq 2:18 or resseq 20:33 or resseq...D1 - 99
312(chain F and (resseq 2 or (resid 3 and (name...F2
322(chain F and (resseq 2 or (resid 3 and (name...F3
332(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
342(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
352(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
362(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
372(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
382(chain F and (resseq 2 or (resid 3 and (name...F1 - 99
412(chain H and (resseq 2 or (resid 3 and (name...H2
422(chain H and (resseq 2 or (resid 3 and (name...H3
432(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
442(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
452(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
462(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
472(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
482(chain H and (resseq 2 or (resid 3 and (name...H1 - 99
113(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 8
123(chain Q and (resseq 1:8 or (resid 9 and (name...Q9
133(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
143(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
153(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
163(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
173(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
183(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
193(chain Q and (resseq 1:8 or (resid 9 and (name...Q1 - 10
213(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 8
223(chain P and (resseq 1:8 or (resid 9 and (name...P9
233(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
243(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
253(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
263(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
273(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
283(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
293(chain P and (resseq 1:8 or (resid 9 and (name...P1 - 10
313(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 8
323(chain R and (resseq 1:8 or (resid 9 and (name...R9
333(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
343(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
353(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
363(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
373(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
383(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
393(chain R and (resseq 1:8 or (resid 9 and (name...R1 - 10
413(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 8
423(chain S and (resseq 1:8 or (resid 9 and (name...S9
433(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
443(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
453(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
463(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
473(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
483(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10
493(chain S and (resseq 1:8 or (resid 9 and (name...S1 - 10

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

-
Protein/peptide , 1 types, 4 molecules PQRS

#3: Protein/peptide
Pre-glycoprotein polyprotein GP complex


Mass: 1147.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P09991

-
Non-polymers , 3 types, 301 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Ammonium Sulfate, 100 mM Tris-HCl, 25% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→19.61 Å / Num. obs: 84550 / % possible obs: 94.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N5A

1n5a


Resolution: 2.4→19.45 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 4220 4.99 %Random
Rwork0.1994 ---
obs0.2024 84550 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 205.33 Å2 / Biso mean: 67.8522 Å2 / Biso min: 29.04 Å2
Refinement stepCycle: final / Resolution: 2.4→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12264 0 155 273 12692
Biso mean--95.71 56.38 -
Num. residues----1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112826
X-RAY DIFFRACTIONf_angle_d1.24117459
X-RAY DIFFRACTIONf_chiral_restr0.0641768
X-RAY DIFFRACTIONf_plane_restr0.0092260
X-RAY DIFFRACTIONf_dihedral_angle_d18.4737536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4082X-RAY DIFFRACTION9.74TORSIONAL
12C4082X-RAY DIFFRACTION9.74TORSIONAL
13E4082X-RAY DIFFRACTION9.74TORSIONAL
14G4082X-RAY DIFFRACTION9.74TORSIONAL
21B1732X-RAY DIFFRACTION9.74TORSIONAL
22D1732X-RAY DIFFRACTION9.74TORSIONAL
23F1732X-RAY DIFFRACTION9.74TORSIONAL
24H1732X-RAY DIFFRACTION9.74TORSIONAL
31Q168X-RAY DIFFRACTION9.74TORSIONAL
32P168X-RAY DIFFRACTION9.74TORSIONAL
33R168X-RAY DIFFRACTION9.74TORSIONAL
34S168X-RAY DIFFRACTION9.74TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42720.39971350.34762463259891
2.4272-2.45570.40351240.33632589271394
2.4557-2.48560.38221230.30342633275699
2.4856-2.5170.33141490.29127762925100
2.517-2.55010.35511420.299926232765100
2.5501-2.58490.35371580.283727172875100
2.5849-2.62180.36161300.293826532783100
2.6218-2.66080.33851350.283827462881100
2.6608-2.70230.35021450.272726872832100
2.7023-2.74650.3671200.272627132833100
2.7465-2.79370.35211550.271827092864100
2.7937-2.84440.32291530.265126992852100
2.8444-2.89890.32171410.244726542795100
2.8989-2.95790.28851520.24327492901100
2.9579-3.02190.32951290.245926862815100
3.0219-3.0920.31751430.242626912834100
3.092-3.1690.33131110.240127512862100
3.169-3.25430.33731180.230226972815100
3.2543-3.34960.28011660.224426942860100
3.3496-3.45710.30761520.21327072859100
3.4571-3.57990.23481330.198227162849100
3.5799-3.72230.23681310.183927672898100
3.7223-3.89040.2831660.180526622828100
3.8904-4.09380.23661510.172827062857100
4.0938-4.34760.19871330.149227022835100
4.3476-4.67890.20091580.137726642822100
4.6789-5.14190.18221430.131327342877100
5.1419-5.8680.18661620.154726832845100
5.868-7.32670.2481370.18727402877100
7.3267-19.45050.22071250.19062319244484
Refinement TLS params.Method: refined / Origin x: -1.7349 Å / Origin y: -13.288 Å / Origin z: 0.0355 Å
111213212223313233
T0.3911 Å20.0009 Å2-0.0017 Å2-0.3813 Å2-0.0423 Å2--0.2943 Å2
L0.5678 °2-0.0031 °2-0.0154 °2-0.3661 °2-0.172 °2---0.0368 °2
S0.0249 Å °0.0049 Å °-0.0028 Å °-0.0012 Å °-0.0202 Å °0.0033 Å °0.0061 Å °-0.0009 Å °-0.0042 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 276
2X-RAY DIFFRACTION1allB1 - 99
3X-RAY DIFFRACTION1allC1 - 276
4X-RAY DIFFRACTION1allD1 - 99
5X-RAY DIFFRACTION1allE1 - 276
6X-RAY DIFFRACTION1allF1 - 99
7X-RAY DIFFRACTION1allG1 - 276
8X-RAY DIFFRACTION1allH1 - 99
9X-RAY DIFFRACTION1allP1 - 10
10X-RAY DIFFRACTION1allQ1 - 10
11X-RAY DIFFRACTION1allR1 - 10
12X-RAY DIFFRACTION1allS1 - 10
13X-RAY DIFFRACTION1allI1 - 5
14X-RAY DIFFRACTION1allI6 - 15
15X-RAY DIFFRACTION1allI16
16X-RAY DIFFRACTION1allI17 - 19
17X-RAY DIFFRACTION1allX1 - 17
18X-RAY DIFFRACTION1allY1 - 299

+
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