[English] 日本語
Yorodumi
- PDB-8tbh: Tricomplex of RMC-7977, KRAS G12R, and CypA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tbh
TitleTricomplex of RMC-7977, KRAS G12R, and CypA
Components
  • GTPase KRas
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsHYDROLASE/INHIBITOR / inhibitor / complex / small GTPase / cancer / tricomplex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / virion binding / Basigin interactions / forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / cyclosporin A binding / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Rac protein signal transduction / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Integration of provirus / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / APOBEC3G mediated resistance to HIV-1 infection / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / Calcineurin activates NFAT / SOS-mediated signalling / viral release from host cell / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / Binding and entry of HIV virion / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / positive regulation of viral genome replication / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / protein peptidyl-prolyl isomerization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / positive regulation of protein dephosphorylation / Signaling by CSF3 (G-CSF) / positive regulation of glial cell proliferation / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / activation of protein kinase B activity / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / neutrophil chemotaxis / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of protein phosphorylation / VEGFR2 mediated cell proliferation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / GTPase KRas / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBar Ziv, T. / Zhang, D. / Tomlinson, A.C.A. / Knox, J.E. / Yano, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2024
Title: Concurrent inhibition of oncogenic and wild-type RAS-GTP for cancer therapy.
Authors: Holderfield, M. / Lee, B.J. / Jiang, J. / Tomlinson, A. / Seamon, K.J. / Mira, A. / Patrucco, E. / Goodhart, G. / Dilly, J. / Gindin, Y. / Dinglasan, N. / Wang, Y. / Lai, L.P. / Cai, S. / ...Authors: Holderfield, M. / Lee, B.J. / Jiang, J. / Tomlinson, A. / Seamon, K.J. / Mira, A. / Patrucco, E. / Goodhart, G. / Dilly, J. / Gindin, Y. / Dinglasan, N. / Wang, Y. / Lai, L.P. / Cai, S. / Jiang, L. / Nasholm, N. / Shifrin, N. / Blaj, C. / Shah, H. / Evans, J.W. / Montazer, N. / Lai, O. / Shi, J. / Ahler, E. / Quintana, E. / Chang, S. / Salvador, A. / Marquez, A. / Cregg, J. / Liu, Y. / Milin, A. / Chen, A. / Ziv, T.B. / Parsons, D. / Knox, J.E. / Klomp, J.E. / Roth, J. / Rees, M. / Ronan, M. / Cuevas-Navarro, A. / Hu, F. / Lito, P. / Santamaria, D. / Aguirre, A.J. / Waters, A.M. / Der, C.J. / Ambrogio, C. / Wang, Z. / Gill, A.L. / Koltun, E.S. / Smith, J.A.M. / Wildes, D. / Singh, M.
History
DepositionJun 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: 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 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTPase KRas
B: GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
D: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,98810
Polymers75,1654
Non-polymers2,8236
Water10,593588
1
A: GTPase KRas
D: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9945
Polymers37,5832
Non-polymers1,4123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9945
Polymers37,5832
Non-polymers1,4123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.418, 85.673, 127.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19458.979 Da / Num. of mol.: 2 / Mutation: G12R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, small monomeric GTPase
#2: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18123.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase

-
Non-polymers , 4 types, 594 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZNI / (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide / RMC-7977


Mass: 865.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H60N8O6S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 17% PEG4000, 0.1 M imidazole, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95375 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 1.5→63.77 Å / Num. obs: 116906 / % possible obs: 99.75 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1048 / Rpim(I) all: 0.04139 / Rrim(I) all: 0.1129 / Net I/σ(I): 7.51
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 7.5 % / Rmerge(I) obs: 2.692 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 11564 / CC1/2: 0.37 / CC star: 0.735 / Rpim(I) all: 1.035 / Rrim(I) all: 2.888 / % possible all: 99.25

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
HKL-2000data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→63.77 Å / SU ML: 0.2456 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 5937 5.09 %
Rwork0.1959 110773 -
obs0.1974 116710 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.51 Å2
Refinement stepCycle: LAST / Resolution: 1.5→63.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 124 588 6002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565564
X-RAY DIFFRACTIONf_angle_d0.80927533
X-RAY DIFFRACTIONf_chiral_restr0.0753808
X-RAY DIFFRACTIONf_plane_restr0.0052967
X-RAY DIFFRACTIONf_dihedral_angle_d13.36132135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.42292220.38933529X-RAY DIFFRACTION96.85
1.52-1.530.34161780.36473655X-RAY DIFFRACTION99.3
1.53-1.550.37881880.35533652X-RAY DIFFRACTION99.43
1.55-1.570.37232020.34443639X-RAY DIFFRACTION99.53
1.57-1.590.34522020.32763644X-RAY DIFFRACTION99.61
1.59-1.620.30921930.30673664X-RAY DIFFRACTION99.66
1.62-1.640.31951900.30073634X-RAY DIFFRACTION99.74
1.64-1.660.40022090.30933671X-RAY DIFFRACTION99.77
1.66-1.690.35411950.29173658X-RAY DIFFRACTION99.79
1.69-1.720.30441620.27253671X-RAY DIFFRACTION99.61
1.72-1.750.26531900.25383707X-RAY DIFFRACTION99.64
1.75-1.780.28511950.24343650X-RAY DIFFRACTION99.77
1.78-1.810.28891730.23863657X-RAY DIFFRACTION99.74
1.81-1.850.26651960.23293711X-RAY DIFFRACTION99.8
1.85-1.890.27761900.22213642X-RAY DIFFRACTION99.69
1.89-1.930.24121970.21563664X-RAY DIFFRACTION99.51
1.93-1.980.23691980.2063686X-RAY DIFFRACTION99.87
1.98-2.030.27111970.2133678X-RAY DIFFRACTION99.95
2.03-2.090.24631890.20963724X-RAY DIFFRACTION99.87
2.09-2.160.24691910.20133692X-RAY DIFFRACTION99.92
2.16-2.240.23282080.19713683X-RAY DIFFRACTION99.9
2.24-2.330.24052060.19723712X-RAY DIFFRACTION99.97
2.33-2.440.22411910.19483703X-RAY DIFFRACTION99.92
2.44-2.560.24292010.19633719X-RAY DIFFRACTION99.95
2.56-2.720.24342020.1973712X-RAY DIFFRACTION99.95
2.72-2.930.23462070.18683746X-RAY DIFFRACTION99.92
2.93-3.230.20142100.18273730X-RAY DIFFRACTION100
3.23-3.70.19952300.16893766X-RAY DIFFRACTION99.97
3.7-4.660.15662280.14333783X-RAY DIFFRACTION99.95
4.66-63.770.17891970.16183991X-RAY DIFFRACTION99.83
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)
13.862268291220.5980225229860.741013753373.024269686741.323541033484.07600024666-0.0348076962674-0.0651524500072-0.008066140592850.159943895108-0.0322992768087-0.2174263341990.02862167170720.1473104801290.0292045540410.168888378422-0.006859289051210.007114489111030.179237801340.04174579709740.130984976288-15.8856370157-9.619172077613.0929846835
23.494161057852.92456220933-2.975044727725.43490627426-0.3248524984554.00201458813-0.1214270174550.356430835157-0.548001219699-0.476229661708-0.22244293672-0.4977463251890.1517344010130.3788245946830.2898197779770.24800380050.05978365173390.03465137628840.3616354882810.02016265989730.196742891584-15.158838942-19.46061491014.52220767533
36.465486659463.151279463440.878435406494.90628636303-0.3007538979843.970476652490.202642113327-0.3472586274520.4015880995420.56662741316-0.363964339307-0.012439765926-0.2134703517830.42564825350.1123543657180.204777685946-0.0324461616005-0.01154283039140.303427295624-0.03813643913380.15611915529-11.7183589136-7.2218037830117.8362925488
47.034755748273.73254952966-0.455927689452.082450976411.565371009160.5769256764660.197263247799-0.2767324327370.1382343554810.217070518204-0.1746909829920.4119803366170.0281297812353-0.3545496921710.08247854685250.2471934116040.02225657507280.0003188967028270.2694702055960.05154763908630.201643035848-30.3114529371-15.118388666317.24271383
52.18681142497-0.151844161347-0.8190090065192.973587345980.9603031531116.37841269377-0.05771806617660.0177360752580.2563575015480.143560842721-0.0001582961460050.653900636671-0.258558827286-0.7483718577030.0661790148070.1888282577180.06224405120030.03496830645880.2854641673290.01003303800170.277568689449-29.273587929-4.5153356129810.6083424446
63.81727284313-0.464842510284-1.426515116192.780082581690.9688436411444.209844651220.1502269601220.7371906083160.496893541606-0.53188512953-0.09142510761360.172882805664-0.516455008815-0.431886012401-0.06985276356380.2991270400790.0419500247399-0.004060075292170.3403854029850.09019268267970.222554799885-22.4603871786-1.44528804448-0.369994823749
79.96700516129-3.08344227961-2.984243820649.26928072272.882896237562.05961797290.0790554406275-0.4618494805071.157439482110.1669441765660.0886853334296-0.0609822554777-0.9680041896030.254943447942-0.149871043360.358107560516-0.0378164904242-0.009809339727550.221578718216-0.03135940600990.290705145945-16.45265365282.9963770658415.9554620638
83.100516268322.861473010340.71409206384.908277189991.409284564752.027787634770.3792282216890.039328822841-0.2558911015070.697330646144-0.184285905717-0.5781871732610.0542791018674-0.0416926718197-0.216397812510.395856970669-0.0800416109225-0.0715316765240.2906254485550.04347266294190.189146180695-17.6292076289-27.728731920235.8578567705
90.5150816768-0.198115495192-0.6048755365640.06473703962410.2024904388320.6567342266130.184405773016-0.122626526427-1.076882100080.6089325181450.0381825669265-1.365417161820.554351079850.167463931578-0.267976194110.512467790702-0.0416690213521-0.2961906954270.361274463294-0.007222818835960.87411667997-4.9399612975-30.463468135935.8527811315
104.639466920194.06785329691-0.2602623419725.40894135343-0.475934188032.283670282150.03736842420250.1033563098440.01760073938310.264462471190.04491222036390.0850183523945-0.00890342059693-0.152682765431-0.1091595949960.260071772498-0.0278644931454-0.009334348787920.275438083425-0.002556103440280.159164471689-21.5946866052-28.299544076432.42768902
1110.00274970135.44851850659-1.228366930325.707319376171.620390942012.000281909070.235178286553-0.2456820310890.7366860151350.734440430052-0.102369596648-0.0960014862914-0.468969864570.441469088793-0.05308817614780.564284628982-0.00992066666894-0.09107219547880.3389369736940.01080696410460.336436135106-15.1737236336-11.803547712737.350334246
123.236486669241.285271591142.589322468162.941676421960.1385248277763.630293353860.73538261824-0.8676451192410.4183372916581.47701745725-0.723937463156-0.00867623737553-0.286517526763-0.2956608592680.131792377770.957002166625-0.260306434148-0.09157011209350.494490362147-0.02683711983540.209552732874-17.0214540963-18.201919875147.6045406818
131.364918410591.720096771631.652962877863.257446983520.6356280408413.809459875780.419832378939-0.7730162644860.8232672802711.1351939892-0.6007170547170.277792725641-0.340489992237-0.6903305929590.1260062668460.929256301356-0.2305884518980.07334100570960.579029491215-0.06982770663410.198609942518-24.6228176911-20.40838983646.4271990062
140.874226361754-1.26552318511.689253165061.83249312221-2.43240948913.23162530494-0.0443398059842-0.648289540804-0.4594577020940.9010249463730.3749463101630.1435372733770.264348498568-0.181052198076-0.3665004574111.53217986616-0.203936274538-0.8027859100130.6243116449190.3832275458660.683851563173-9.13292603798-32.379529518654.7506538346
152.49742475369-0.1817304706260.2291233659811.668004480121.583710825187.098070206870.169622947887-1.14586228619-0.3534833085230.973705517866-0.06118506353380.0667657398540.896938645698-0.547181321627-0.08477596110731.54878657254-0.6036308481710.2117196418841.13209001697-0.1294906035820.073609073379-22.0430016574-24.539389677457.798475876
164.81819326558-1.47936913275-1.504654630573.721016469590.898531631013.172266505180.62605242529-0.773474801785-0.5578402908481.37174581251-0.239236511083-0.6298948657860.630814632791-0.153888523955-0.2655783343851.19111686538-0.377651313764-0.4439627127920.404845227390.4412229057790.123879346089-17.0955355506-33.890223939147.0447867238
178.681550955320.1412208360131.326557919585.985427201080.06647725599966.434697955780.505763827858-0.836766811287-0.1743817178280.838067374468-0.4467001690750.5246121221210.0524413628617-0.960171708271-0.06264286577640.537364441071-0.194541274890.08273907836650.500510892766-0.004552727549440.222256516092-29.5883379153-28.701798873141.2349416195
185.901226604742.171463956572.825109174215.092161712442.827287026656.236769379690.1833046420550.469318005732-0.0227038805539-0.2543702244850.0134769295768-0.4471550552020.1807963923780.661756636073-0.14311200220.2326724607360.02855785111880.01255214458580.344285448188-0.02307817616730.217402261114.8447887698-16.292406455318.34770776
192.43243816714-0.1457700174280.7190814940842.915738811120.2513485066784.306574731030.04306223864430.183776485843-0.06510498261610.124387462794-0.00906967657151-0.4391292491680.1400316542790.371826355122-0.02340851778340.1661513903590.0110377787215-0.03566435460630.316815916047-0.03181042156540.23085955337817.2298410702-14.418577658125.3044856347
202.97651576489-1.07502786220.7471343621482.721654528970.08430842902161.741476217120.1447505585730.345857737408-0.1909270226530.0566084782263-0.0407861334832-0.22188814480.319437212330.105401031798-0.1398425444380.2627832666740.0206301062139-0.05096014739320.24158641117-0.03116564452940.1849963409687.31075226545-20.341871708825.0088014853
212.00700312648-1.37631275905-3.419872533094.713837123911.643843159735.545066295230.1319375365940.280651608639-1.10062163868-0.144844946423-0.1217060749130.1276220874560.730442297207-0.0461181324675-0.04481535512290.4255034821770.00320982416519-0.1298950927050.320400735233-0.07600766951860.427761979446.2754435215-28.459957857629.4285686966
225.2682698121-2.41738906927-1.517627284382.887190200813.956195745456.368017680940.197613498705-0.662938623041-0.5403230568670.9391602094060.0274523000081-0.3800413529840.810762862430.305540865135-0.1266805502030.4141177620590.0388390756936-0.1963448374650.3238128560880.0393328782850.41847511415815.6331406855-23.113980173137.738640494
233.195981344730.01026376258470.9552826807972.117776526610.09262238465652.127067460750.0227885454837-0.009960134438740.1392226300280.190295052568-0.048753397146-0.109496149358-0.04459617372280.08400990966410.02742741594290.226486106065-0.0341921509794-0.04799741587620.203226543108-0.01696699780810.1604510314517.3617239202-10.512178006633.417615736
242.83713588828-0.3615597508491.030651556473.475375909291.63564012444.743549861220.08249118958620.2608121626930.03013072669840.141876319903-0.0298930480122-0.189356924954-0.4152930664980.230470601145-0.02536879143720.219515679017-0.0130189772247-0.06958130392370.220476408988-0.006344540238270.18014404412510.58309486-8.3360373407229.0283956905
259.956860322196.59151372309-4.027467626629.06792906797-1.215857128863.87828550628-0.2707995956220.7268042336910.171647466327-0.3757803969890.2629252190320.339456341382-0.069040136245-0.544167313546-0.04447973483360.3246829684820.0309131929998-0.01188110971330.381869379624-0.001501568850510.1280679596112.25139663733-12.078782334315.4151260054
262.19706471852-0.671595431385-0.4557911932082.154026534080.5520128803592.891809697580.1687165869040.733739780977-0.452661067295-0.0761261710265-0.09926887119960.04102247324170.349742635915-0.191544449456-0.08008439743080.2642070056930.0236161801769-0.06189843879350.337778167861-0.07503920755680.1681184653444.02534507901-20.482659529919.6105001007
272.92833297458-1.289555165971.089891727592.28983812218-0.2872482932472.817068187770.209842451780.191001630966-0.4467691144630.00862500783015-0.0132587554306-0.1912822371980.5700099747230.230894355733-0.1905960103220.2651231563890.0611172899524-0.009552108367080.203475014258-0.01905081513980.177644560285-19.4598096026-47.877036285410.9350224546
282.58997904017-0.2064514422220.4249960506552.69013506566-0.8129555359623.460658908390.03064982334290.162139338787-0.236186151038-0.1822302068110.0428240508246-0.05114589817150.415176468361-0.009756789467460.002057516668470.2306988930280.0234253750608-0.03472465890590.167952879223-0.04200691190560.164921822059-25.4517520729-46.56895027626.2376367242
291.50116346575-0.17507347841-1.2232828931.736876277111.198169519173.394202997210.00058067542250.0509908378905-0.134235364128-0.06133618052410.000495544455286-0.1142728024470.09999161859390.183055161455-0.007113657415340.2054222953470.0429308493402-0.01132318900620.2569343799680.003012866635970.139005126106-19.1807799476-37.37943198149.0827775123
306.31393188294-0.559772145188-2.173032104522.007784896424.990188801954.622555601940.01172233523490.2376636769390.18542792859-0.070494623688-0.0314788859711-0.591135212486-0.26168101810.13825617897-0.0007216629887840.2632281184260.007212804682590.01002511957870.3137799897040.0005269555529430.218153016894-14.8375438671-32.22367197212.78761472786
314.19653778567-0.547662342027-0.24894575053.028586693490.005980705694366.79350647816-0.09306404993350.2703076104440.189338722031-0.2515907271920.0670119659518-0.0150389717965-0.02431629772780.3332017458550.0224929467390.2438746390790.0226388372607-0.009320946874990.322269668294-0.01819842505940.134456181604-24.9937071019-36.2281248156-4.92345863548
322.167235903480.4307367011660.8876306525791.2823268970.08734607719842.391054509620.0948993959733-0.032199521697-0.005539426552820.02972642035610.04720267325820.1225442978310.115914703207-0.11947537376-0.1042970348250.1652469430260.0141430455167-0.01602662397720.1917988176310.01246165030810.125560166992-31.9849463994-35.16505872228.88811813535
335.60840742478-1.527217414552.329273274222.56331595186-1.221533928715.759282782660.121576984554-0.0509822737517-0.456413368481-0.04759057736210.1661001606010.372570698920.428739372881-0.128969712899-0.2796011119530.16541502589-0.0221562765406-0.017638471380.1611193306730.0132059318840.115054622976-31.4051393077-41.634335442911.1016627712
345.73721802213.8405784586-0.4565840639178.194418527060.3868057071343.105369173140.164412845802-0.392298717701-0.09342117087350.222716047254-0.05465810966-0.1466413451810.1374520379980.0217148360657-0.06610189815640.2059898369250.0611976718032-0.06684515611220.2696989124380.05125745399330.194780846278-19.7309449286-40.73947327122.2681878882
351.8279494415-0.1520582278711.130195417836.517669114082.823879694673.873892072290.01157813635880.0831951278423-0.01306814041580.3388473950670.0371584911354-0.4303863871990.1642779402930.245533618891-0.1048729721520.1638958551880.0228996049672-0.01663195309250.2427659319930.01407776377750.120772050114-15.6124101997-37.741089766914.2412735985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 58 )
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 151 )
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 169 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 36 )
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 74 )
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 116 )
14X-RAY DIFFRACTION14chain 'B' and (resid 117 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 137 )
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 151 )
17X-RAY DIFFRACTION17chain 'B' and (resid 152 through 169 )
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 14 )
19X-RAY DIFFRACTION19chain 'C' and (resid 15 through 41 )
20X-RAY DIFFRACTION20chain 'C' and (resid 42 through 64 )
21X-RAY DIFFRACTION21chain 'C' and (resid 65 through 74 )
22X-RAY DIFFRACTION22chain 'C' and (resid 75 through 84 )
23X-RAY DIFFRACTION23chain 'C' and (resid 85 through 122 )
24X-RAY DIFFRACTION24chain 'C' and (resid 123 through 135 )
25X-RAY DIFFRACTION25chain 'C' and (resid 136 through 145 )
26X-RAY DIFFRACTION26chain 'C' and (resid 146 through 164 )
27X-RAY DIFFRACTION27chain 'D' and (resid 2 through 14 )
28X-RAY DIFFRACTION28chain 'D' and (resid 15 through 41 )
29X-RAY DIFFRACTION29chain 'D' and (resid 42 through 64 )
30X-RAY DIFFRACTION30chain 'D' and (resid 65 through 74 )
31X-RAY DIFFRACTION31chain 'D' and (resid 75 through 84 )
32X-RAY DIFFRACTION32chain 'D' and (resid 85 through 122 )
33X-RAY DIFFRACTION33chain 'D' and (resid 123 through 135 )
34X-RAY DIFFRACTION34chain 'D' and (resid 136 through 145 )
35X-RAY DIFFRACTION35chain 'D' and (resid 146 through 164 )

+
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