[English] 日本語
Yorodumi
- PDB-7jxh: HER2 in complex with JBJ-08-178-01 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jxh
TitleHER2 in complex with JBJ-08-178-01
ComponentsReceptor tyrosine-protein kinase erbB-2
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / HER2 / ErbB2 / kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / RNA polymerase I core binding / immature T cell proliferation in thymus / semaphorin receptor complex / ErbB-3 class receptor binding / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / RNA polymerase I core binding / immature T cell proliferation in thymus / semaphorin receptor complex / ErbB-3 class receptor binding / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse / regulation of microtubule-based process / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / enzyme-linked receptor protein signaling pathway / ERBB2 Activates PTK6 Signaling / neuromuscular junction development / ERBB2-ERBB3 signaling pathway / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / positive regulation of Rho protein signal transduction / positive regulation of MAP kinase activity / positive regulation of transcription by RNA polymerase I / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / oligodendrocyte differentiation / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / Schwann cell development / coreceptor activity / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / transmembrane receptor protein tyrosine kinase activity / GRB2 events in ERBB2 signaling / positive regulation of cell adhesion / SHC1 events in ERBB2 signaling / cell surface receptor protein tyrosine kinase signaling pathway / Downregulation of ERBB2:ERBB3 signaling / basal plasma membrane / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Overexpressed ERBB2 / cellular response to epidermal growth factor stimulus / positive regulation of translation / positive regulation of epithelial cell proliferation / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / cellular response to growth factor stimulus / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / early endosome / cell surface receptor signaling pathway / cell population proliferation / protein phosphorylation / receptor complex / positive regulation of MAPK cascade / endosome membrane / intracellular signal transduction / apical plasma membrane / protein heterodimerization activity / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-VOY / Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsBeyett, T.S. / Eck, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA201049-05 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1F32CA247198-01 United States
CitationJournal: Cancer Res. / Year: 2022
Title: A Novel HER2-Selective Kinase Inhibitor Is Effective in HER2 Mutant and Amplified Non-Small Cell Lung Cancer.
Authors: Son, J. / Jang, J. / Beyett, T.S. / Eum, Y. / Haikala, H.M. / Verano, A. / Lin, M. / Hatcher, J.M. / Kwiatkowski, N.P. / Eser, P.O. / Poitras, M.J. / Wang, S. / Xu, M. / Gokhale, P.C. / ...Authors: Son, J. / Jang, J. / Beyett, T.S. / Eum, Y. / Haikala, H.M. / Verano, A. / Lin, M. / Hatcher, J.M. / Kwiatkowski, N.P. / Eser, P.O. / Poitras, M.J. / Wang, S. / Xu, M. / Gokhale, P.C. / Cameron, M.D. / Eck, M.J. / Gray, N.S. / Janne, P.A.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Receptor tyrosine-protein kinase erbB-2
A: Receptor tyrosine-protein kinase erbB-2
C: Receptor tyrosine-protein kinase erbB-2
D: Receptor tyrosine-protein kinase erbB-2
E: Receptor tyrosine-protein kinase erbB-2
F: Receptor tyrosine-protein kinase erbB-2
G: Receptor tyrosine-protein kinase erbB-2
H: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,57716
Polymers295,0768
Non-polymers4,5018
Water00
1
B: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.138, 154.617, 93.548
Angle α, β, γ (deg.)90.000, 102.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 713 through 740 or resid 746...
21(chain B and (resid 713 through 740 or resid 746...
31(chain C and (resid 713 through 740 or resid 746...
41(chain D and (resid 713 through 740 or resid 746...
51(chain E and (resid 713 through 740 or resid 746...
61(chain F and (resid 713 through 763 or resid 765...
71(chain G and (resid 713 through 740 or resid 746...
81(chain H and (resid 713 through 740 or resid 746...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 713 through 740 or resid 746...A713 - 740
121(chain A and (resid 713 through 740 or resid 746...A746 - 763
131(chain A and (resid 713 through 740 or resid 746...A765 - 856
141(chain A and (resid 713 through 740 or resid 746...A858 - 867
151(chain A and (resid 713 through 740 or resid 746...A975 - 991
161(chain A and (resid 713 through 740 or resid 746...A1001
211(chain B and (resid 713 through 740 or resid 746...B713 - 740
221(chain B and (resid 713 through 740 or resid 746...B746 - 763
231(chain B and (resid 713 through 740 or resid 746...B707 - 1001
241(chain B and (resid 713 through 740 or resid 746...B975 - 99
251(chain B and (resid 713 through 740 or resid 746...B975 - 991
261(chain B and (resid 713 through 740 or resid 746...B1001
311(chain C and (resid 713 through 740 or resid 746...C713 - 740
321(chain C and (resid 713 through 740 or resid 746...C746 - 763
331(chain C and (resid 713 through 740 or resid 746...C765 - 856
341(chain C and (resid 713 through 740 or resid 746...C858 - 867
351(chain C and (resid 713 through 740 or resid 746...C975 - 991
361(chain C and (resid 713 through 740 or resid 746...C1001
411(chain D and (resid 713 through 740 or resid 746...D713 - 740
421(chain D and (resid 713 through 740 or resid 746...D746 - 763
431(chain D and (resid 713 through 740 or resid 746...D765 - 856
441(chain D and (resid 713 through 740 or resid 746...D858 - 867
451(chain D and (resid 713 through 740 or resid 746...D975 - 991
461(chain D and (resid 713 through 740 or resid 746...D1001
511(chain E and (resid 713 through 740 or resid 746...E713 - 740
521(chain E and (resid 713 through 740 or resid 746...E746 - 763
531(chain E and (resid 713 through 740 or resid 746...E709 - 992
541(chain E and (resid 713 through 740 or resid 746...E858 - 867
551(chain E and (resid 713 through 740 or resid 746...E975 - 991
561(chain E and (resid 713 through 740 or resid 746...E1001
611(chain F and (resid 713 through 763 or resid 765...F713 - 763
621(chain F and (resid 713 through 763 or resid 765...F765 - 856
631(chain F and (resid 713 through 763 or resid 765...F713 - 1001
641(chain F and (resid 713 through 763 or resid 765...F885 - 973
651(chain F and (resid 713 through 763 or resid 765...F975 - 1001
711(chain G and (resid 713 through 740 or resid 746...G713 - 740
721(chain G and (resid 713 through 740 or resid 746...G746 - 763
731(chain G and (resid 713 through 740 or resid 746...G765 - 856
741(chain G and (resid 713 through 740 or resid 746...G858 - 867
751(chain G and (resid 713 through 740 or resid 746...G975 - 991
761(chain G and (resid 713 through 740 or resid 746...G1001
811(chain H and (resid 713 through 740 or resid 746...H713 - 740
821(chain H and (resid 713 through 740 or resid 746...H746 - 763
831(chain H and (resid 713 through 740 or resid 746...H765 - 856
841(chain H and (resid 713 through 740 or resid 746...H975 - 99
851(chain H and (resid 713 through 740 or resid 746...H975 - 991
861(chain H and (resid 713 through 740 or resid 746...H1001

-
Components

#1: Protein
Receptor tyrosine-protein kinase erbB-2 / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 36884.512 Da / Num. of mol.: 8 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, MLN19, NEU, NGL / Plasmid: pTriEX / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-VOY / (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide


Mass: 562.622 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H30N8O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.26→91.34 Å / Num. obs: 75837 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 48.579 Å2 / Rpim(I) all: 0.226 / Rrim(I) all: 0.595 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
3.26-3.3270.91260718051.4773.9392.6
8.86-91.226.89.21372520140.0360.09599.6

-
Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP0

3pp0


Resolution: 3.27→91.34 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2849 3908 5.15 %
Rwork0.239 71929 -
obs0.2413 75837 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.27 Å2 / Biso mean: 65.1921 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 3.27→91.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17524 0 336 0 17860
Biso mean--45.76 --
Num. residues----2190
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10107X-RAY DIFFRACTION14.928TORSIONAL
12B10107X-RAY DIFFRACTION14.928TORSIONAL
13C10107X-RAY DIFFRACTION14.928TORSIONAL
14D10107X-RAY DIFFRACTION14.928TORSIONAL
15E10107X-RAY DIFFRACTION14.928TORSIONAL
16F10107X-RAY DIFFRACTION14.928TORSIONAL
17G10107X-RAY DIFFRACTION14.928TORSIONAL
18H10107X-RAY DIFFRACTION14.928TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.27-3.310.32031410.3203246596
3.31-3.350.38831180.3503259798
3.35-3.40.38071460.345254298
3.4-3.440.37231370.3292256898
3.44-3.490.32661360.3176257299
3.49-3.540.31921310.3018256098
3.54-3.60.35511520.3032260898
3.6-3.660.30991440.3099254498
3.66-3.720.42431280.3048257498
3.72-3.790.33981470.2968255396
3.79-3.860.311370.2609254099
3.86-3.940.30871490.2636258899
3.94-4.030.32731400.25022580100
4.03-4.120.29041380.2463262299
4.12-4.220.28521420.2234257299
4.22-4.340.24861450.2118259199
4.34-4.460.2771420.214258699
4.46-4.610.24421320.1966258799
4.61-4.770.21831350.1882258298
4.77-4.960.26991400.2011252496
4.96-5.190.24181290.1982256898
5.19-5.460.26971410.2039260499
5.46-5.810.28311470.22012600100
5.81-6.250.24261480.2072257599
6.25-6.880.27291350.2086258999
6.88-7.880.23591380.2124254797
7.88-9.920.21531480.1666255899
9.93-91.340.24471420.2127253396
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4633-0.11620.76336.26262.13841.89650.0597-0.203-0.0003-0.1355-0.03210.0574-0.0815-0.1021-0.08140.3478-0.04850.0340.43640.04620.327230.8954.97241.619
21.78-0.6023-0.59475.59380.68122.98590.07130.0130.14250.2853-0.02760.0940.1758-0.0378-0.05460.2818-0.0734-0.06690.36710.07860.290765.0545.05176.392
31.3167-1.8533-0.46556.49911.42232.2814-0.13150.0566-0.0278-0.20880.08950.04660.10180.00290.01650.3757-0.1045-0.04660.38340.05420.401420.769-1.95586.023
41.0117-2.0079-0.3785.77290.83292.1620.01690.1205-0.0513-0.2726-0.03180.16150.01270.03810.03550.3051-0.0399-0.02760.35950.03350.255876.536-2.35330.099
52.5305-2.81020.29256.0818-0.61281.9987-0.02210.03590.08370.1294-0.01340.2112-0.2421-0.1080.07510.2556-0.0169-0.01580.3878-0.06260.328739.71843.75175.95
61.82030.81790.0815.4110.52641.7133-0.16410.00620.1774-0.25640.11950.7092-0.2424-0.08480.04220.46350.06340.04080.39310.06530.323265.648-33.82950.171
71.8331-1.67730.31446.1284-1.56771.4457-0.03080.0571-0.1346-0.31170.1459-0.1142-0.0172-0.054-0.15770.4356-0.07140.09280.4015-0.03630.323951.3836.61431.381
81.5134-0.62140.46994.772-2.12012.72190.0188-0.07780.20240.4382-0.2343-0.441-0.23120.22570.16410.3142-0.0607-0.05090.3285-0.02460.428686.25535.95586.485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND ( RESID 708:996 OR RESID 1101:1101 ) )B708 - 996
2X-RAY DIFFRACTION1( CHAIN B AND ( RESID 708:996 OR RESID 1101:1101 ) )B1101
3X-RAY DIFFRACTION2( CHAIN A AND RESID 706:992 )A706 - 992
4X-RAY DIFFRACTION3( CHAIN C AND RESID 710:992 )C710 - 992
5X-RAY DIFFRACTION4( CHAIN D AND RESID 710:992 )D710 - 992
6X-RAY DIFFRACTION5( CHAIN E AND RESID 709:992 )E709 - 992
7X-RAY DIFFRACTION6( CHAIN F AND ( RESID 713:991 OR RESID 1101:1101 ) )F713 - 991
8X-RAY DIFFRACTION6( CHAIN F AND ( RESID 713:991 OR RESID 1101:1101 ) )F1101
9X-RAY DIFFRACTION7( CHAIN G AND RESID 706:992 )G706 - 992
10X-RAY DIFFRACTION8( CHAIN H AND RESID 707:992 )H707 - 992

+
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