[English] 日本語
Yorodumi
- PDB-4n4s: A Double Mutant Rat Erk2 in Complex With a Pyrazolo[3,4-d]pyrimid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n4s
TitleA Double Mutant Rat Erk2 in Complex With a Pyrazolo[3,4-d]pyrimidine Inhibitor
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine kinase / MAP kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / Recycling pathway of L1 / neural crest cell development / diadenosine tetraphosphate biosynthetic process / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / positive regulation of macrophage proliferation / outer ear morphogenesis / Thrombin signalling through proteinase activated receptors (PARs) / regulation of cellular pH / RAF/MAP kinase cascade / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / : / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / progesterone receptor signaling pathway / androgen receptor signaling pathway / pseudopodium / Bergmann glial cell differentiation / negative regulation of cell differentiation / positive regulation of telomere capping / thyroid gland development / decidualization / steroid hormone receptor signaling pathway / MAP kinase activity / regulation of ossification / phosphatase binding / mitogen-activated protein kinase / Schwann cell development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / sensory perception of pain / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / ERK1 and ERK2 cascade / myelination / cellular response to amino acid starvation / dendrite cytoplasm / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / caveola / positive regulation of translation / long-term synaptic potentiation / animal organ morphogenesis
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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-2H1 / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHari, S.B. / Maly, D.J. / Merritt, E.A.
CitationJournal: Chem.Biol. / Year: 2014
Title: Conformation-Selective ATP-Competitive Inhibitors Control Regulatory Interactions and Noncatalytic Functions of Mitogen-Activated Protein Kinases.
Authors: Hari, S.B. / Merritt, E.A. / Maly, D.J.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
B: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5564
Polymers82,7072
Non-polymers8492
Water1,49583
1
A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7782
Polymers41,3541
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7782
Polymers41,3541
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.090, 57.630, 68.000
Angle α, β, γ (deg.)86.570, 88.980, 81.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 8 - 356 / Label seq-ID: 9 - 357

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2


Mass: 41353.504 Da / Num. of mol.: 2 / Mutation: Q103A/C164L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erk2, Mapk, Mapk1, Prkm1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Chemical ChemComp-2H1 / 3-[2-(benzyloxy)-8-methylquinolin-6-yl]-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 424.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 100 mM CHES, pH 9.5, 30% PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2012
RadiationMonochromator: liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 1.8 % / Av σ(I) over netI: 4.7 / Number: 51072 / Rsym value: 0.109 / D res high: 2.2 Å / D res low: 56.833 Å / Num. obs: 27949 / % possible obs: 79.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.9656.8381.910.0790.0791.9
4.926.9679.910.0820.0821.9
4.024.9280.310.0770.0771.9
3.484.0281.510.0830.0831.8
3.113.4879.510.10.11.8
2.843.1177.110.1050.1051.8
2.632.848310.1350.1351.8
2.462.6375.210.1790.1791.8
2.322.4679.810.2350.2351.8
2.22.3282.110.2860.2861.8
ReflectionResolution: 2.2→67.88 Å / Num. all: 27949 / Num. obs: 27949 / % possible obs: 79.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4179 / % possible all: 82.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å56.83 Å
Translation2.5 Å56.83 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QYW
Resolution: 2.2→56.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2777 / WRfactor Rwork: 0.2398 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8086 / SU B: 16.717 / SU ML: 0.202 / SU R Cruickshank DPI: 0.642 / SU Rfree: 0.2823 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.642 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1400 5 %RANDOM
Rwork0.2208 ---
obs0.2225 27934 79.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.25 Å2 / Biso mean: 45.2142 Å2 / Biso min: 16.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å2-0.25 Å20.79 Å2
2--2.45 Å20.72 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→56.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5509 0 64 83 5656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195716
X-RAY DIFFRACTIONr_bond_other_d0.0030.025510
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9927756
X-RAY DIFFRACTIONr_angle_other_deg0.8063.00312675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9015677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04124.075265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.906151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8861534
X-RAY DIFFRACTIONr_chiral_restr0.0620.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216354
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021308
X-RAY DIFFRACTIONr_mcbond_it0.4741.9562714
X-RAY DIFFRACTIONr_mcbond_other0.4741.9562713
X-RAY DIFFRACTIONr_mcangle_it0.8052.9333386
Refine LS restraints NCS

Ens-ID: 1 / Number: 21456 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 101 -
Rwork0.322 1962 -
all-2063 -
obs--80.43 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.3498-4.875.935334.2999-3.94457.7668-0.5031-0.58060.57791.55540.16850.1814-0.5431-0.31770.33460.2254-0.00880.08090.4021-0.04790.3636-20.504326.185411.2463
21.5783-0.3674.25318.6948-4.367614.4253-0.0013-0.16250.23140.7446-0.4595-0.1877-0.29360.55490.46080.1020.00730.08950.4711-0.01610.3639-18.313430.3934.503
39.3429-8.98522.526613.2104-2.76627.1214-0.3718-0.22890.30470.01530.2408-0.75050.38520.37470.13110.1862-0.03050.12630.19950.01640.2147-16.202219.23084.7716
45.3512.0566-1.65476.0841.45183.77750.0645-0.45660.14230.1489-0.1723-0.18510.10540.24610.10780.06580.02830.07540.1236-0.00940.1935-15.105325.70110.966
56.1005-0.85134.75443.31953.388623.6117-0.0123-0.49510.11050.29880.1421-0.14130.10270.6014-0.12980.15120.00670.01420.0979-0.01330.35831.673424.0794-0.7899
62.884-1.98990.16758.76375.26544.7226-0.0460.22890.5338-0.38160.1945-0.1311-0.34230.2574-0.14850.0854-0.01610.0220.05170.05850.2798-7.415625.7133-8.3229
713.632412.7722-3.88627.1641-16.539712.0583-0.0895-0.07130.25340.9054-0.3295-0.3239-0.81460.28680.4190.3057-0.0021-0.07280.4392-0.05830.4117-4.234938.46228.4275
85.44211.7046-0.89610.55613.86526.3536-0.1315-0.2499-0.1979-0.0067-0.0057-0.204-0.05550.32260.13720.04110.07410.04590.17420.1040.1836-13.844823.3924-1.9236
93.45510.6934-0.20422.90490.49152.2703-0.02370.13180.1293-0.01070.08350.1073-0.0433-0.168-0.05980.06480.0285-0.0080.05960.03240.0862-9.18027.1651-10.0861
1011.51552.5042.46686.43092.588.57230.4821-0.61630.5355-0.0338-0.3197-0.5155-0.07170.3932-0.16240.14140.01240.06930.12470.03940.1789-1.573313.9813-7.9236
115.7865-4.68972.45395.12061.509510.40820.17830.16471.0255-0.56570.142-1.1436-1.42670.6706-0.32030.85930.01870.10630.5724-0.08420.47997.08139.31822.7252
127.68960.4491-6.44153.31470.55775.66130.3748-1.07480.31920.44530.0237-0.4442-0.19740.9256-0.39850.1411-0.0027-0.07060.1783-0.05510.16884.87630.6687-0.8918
131.31222.553-3.80474.9829-7.418711.08350.2629-0.6716-0.22060.3721-1.1837-0.5409-0.39741.96710.92090.72690.0611-0.02130.8018-0.05980.991212.81645.8529-7.6446
1410.6777-0.0531-0.65022.459-0.08372.91610.0754-0.0957-0.1963-0.1018-0.1589-0.02540.15170.04280.08360.03210.0138-0.02070.0304-0.03040.0786-4.5521-1.0156-8.3605
156.19530.33011.68192.1424-0.28051.5890.00950.3644-0.2558-0.21470.0911-0.12010.05950.1284-0.10060.12340.0095-0.01310.0557-0.01870.17378.9023-9.8778-2.8455
165.98440.14070.6662.3944-0.28321.37760.19630.3709-0.1559-0.1896-0.16-0.23420.07750.1209-0.03630.15110.04590.02450.1479-0.04450.1248-1.5623-4.8797-16.6042
179.41614.83865.11919.43195.58618.3329-0.55161.00510.4538-1.28740.5729-0.1483-0.67120.6538-0.02130.2540.02320.11780.38940.13520.1549-2.757113.6988-22.4254
186.8481-2.4621-3.96140.93071.74421.8634-0.1355-0.30750.19270.10640.18350.03170.24050.0095-0.0480.4595-0.0575-0.03210.3368-0.00130.603410.490126.20251.1825
1911.414-8.6861-3.01827.2736-0.06069.2633-0.5053-0.70520.97520.59480.3218-0.8582-0.7550.67920.18340.16440.06-0.12750.4467-0.15670.69453.797333.67454.3403
207.8601-5.39345.3744.5473-2.1526.5126-0.17810.62753.457-0.516-0.7402-3.177-1.189-0.24380.91830.65080.0290.55230.38790.54422.2891-6.297337.5987-5.6284
212.920.802-1.16586.63190.69875.3652-0.2753-0.4831-0.22260.31040.0470.1493-0.1194-0.07640.22820.13020.0488-0.03850.26010.02590.211927.8984-18.7815-23.9101
226.4666-0.1581-0.88485.6885-1.85735.81260.02860.04920.08660.069-0.00140.0418-0.0435-0.3057-0.02720.08090.0026-0.0470.15970.02330.111225.1006-19.9098-29.2519
236.0237-1.9199-6.12392.65152.757220.35520.0646-0.21040.13950.0152-0.04370.5066-0.3878-0.9073-0.02090.20040.0274-0.01090.23210.00650.31647.9791-18.4013-31.8696
241.4891-3.10452.46478.8398-10.213215.13390.0779-0.009-0.0916-0.2896-0.04580.06270.5470.0757-0.03210.137-0.068-0.0710.21850.02530.227717.958-22.1065-36.7679
255.593-3.5009-6.00726.0491-1.34117.5484-0.26190.41430.32631.02720.79320.36980.0812-0.7125-0.53130.3394-0.07990.00530.48550.19090.482613.8801-30.0117-18.8414
260.26290.1412-0.132512.7292-5.16182.1958-0.0213-0.19090.05660.63250.0561-0.0649-0.34560.1456-0.03480.1805-0.1029-0.00560.3751-0.05120.17324.147-8.2805-33.9045
279.21215.01478.10964.784212.078935.97520.2212-0.0250.24480.1920.0811-0.08880.51320.3361-0.30230.2559-0.02110.03840.30290.01250.418828.32245.5689-46.0613
283.26780.25730.73064.1311-0.68284.32590.2049-0.1636-0.16630.1228-0.0883-0.1043-0.02120.2057-0.11650.0792-0.0080.00220.1387-0.00120.057415.9326-6.7045-43.9551
2937.5992-8.98886.23983.70142.786512.99390.15921.15910.7079-0.3755-0.4588-0.043-0.7313-0.46890.29960.4355-0.1142-0.01160.28820.10780.4183-1.6911-10.0207-41.7181
3013.13556.18250.50215.24125.181110.52240.3396-1.50960.18970.7113-0.93380.36351.1269-0.60460.59430.41330.1390.08060.50430.0910.32924.50424.7224-36.1175
310.1452-0.5654-0.03392.67740.13580.0107-0.1538-0.13850.16580.18470.229-0.54170.00960.0338-0.07520.77140.1341-0.06070.8249-0.12810.657-4.2069-0.1461-40.3224
320.8697-0.9094-1.23924.89940.06462.15070.0781-0.1581-0.1365-0.026-0.16210.5547-0.10440.32840.08390.09060.00290.04210.1409-0.01030.16117.71530.2002-45.0347
334.1676-2.9778-1.86523.2368-0.49544.39120.1533-0.28160.2562-0.0260.10560.0384-0.2904-0.1341-0.25890.2516-0.06290.03590.4022-0.14090.2898.149312.5233-39.7484
349.35973.2618-0.1238.11191.67378.7705-0.39020.96480.3631-0.7913-0.01920.6008-0.3609-0.58580.40940.32770.02880.00310.3421-0.0710.3975-10.226611.0104-40.9115
3513.87365.4409-5.59044.4444-4.63694.84990.3601-0.19850.3810.4739-0.06120.2432-0.55460.0289-0.29890.3930.05270.14930.4276-0.00920.40790.511520.2878-43.1056
3613.91114.57022.68066.3694-0.29640.8451-0.18-0.29470.5148-0.07250.10470.1763-0.1658-0.02090.07530.4451-0.19870.08150.33940.05380.11618.002213.9021-51.5395
373.9347-2.6889-1.97036.50211.22151.73090.27560.08310.1679-0.135-0.14670.5455-0.3056-0.1257-0.12890.16550.0060.01350.26920.010.11047.69583.5886-53.2645
381.6068-1.5244-1.10592.6662-0.24795.9872-0.03250.2148-0.3084-0.3125-0.11590.05350.5779-0.25880.14840.1578-0.02040.01180.2215-0.06820.17113.1032-12.2408-54.0384
393.867-2.62313.16171.8037-1.510120.7884-0.00380.12030.41540.0019-0.0778-0.2874-0.24041.18020.08160.4184-0.0770.01390.46460.05210.5583-0.3847-20.8108-27.8323
407.7435-2.47780.548210.4483-1.34485.25710.0650.015-0.4953-0.26520.4790.20390.7929-0.4775-0.5440.2686-0.0854-0.02160.38050.06160.379811.4051-29.8725-29.7337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 13
2X-RAY DIFFRACTION2A14 - 24
3X-RAY DIFFRACTION3A25 - 34
4X-RAY DIFFRACTION4A35 - 59
5X-RAY DIFFRACTION5A60 - 74
6X-RAY DIFFRACTION6A75 - 91
7X-RAY DIFFRACTION7A92 - 97
8X-RAY DIFFRACTION8A98 - 107
9X-RAY DIFFRACTION9A108 - 158
10X-RAY DIFFRACTION10A159 - 173
11X-RAY DIFFRACTION11A174 - 187
12X-RAY DIFFRACTION12A188 - 198
13X-RAY DIFFRACTION13A199 - 205
14X-RAY DIFFRACTION14A206 - 223
15X-RAY DIFFRACTION15A224 - 274
16X-RAY DIFFRACTION16A275 - 311
17X-RAY DIFFRACTION17A312 - 328
18X-RAY DIFFRACTION18A329 - 338
19X-RAY DIFFRACTION19A339 - 346
20X-RAY DIFFRACTION20A347 - 356
21X-RAY DIFFRACTION21B8 - 34
22X-RAY DIFFRACTION22B35 - 59
23X-RAY DIFFRACTION23B60 - 75
24X-RAY DIFFRACTION24B76 - 92
25X-RAY DIFFRACTION25B93 - 97
26X-RAY DIFFRACTION26B98 - 116
27X-RAY DIFFRACTION27B117 - 122
28X-RAY DIFFRACTION28B123 - 168
29X-RAY DIFFRACTION29B169 - 174
30X-RAY DIFFRACTION30B187 - 198
31X-RAY DIFFRACTION31B199 - 204
32X-RAY DIFFRACTION32B205 - 215
33X-RAY DIFFRACTION33B216 - 248
34X-RAY DIFFRACTION34B249 - 261
35X-RAY DIFFRACTION35B262 - 272
36X-RAY DIFFRACTION36B273 - 285
37X-RAY DIFFRACTION37B286 - 310
38X-RAY DIFFRACTION38B311 - 328
39X-RAY DIFFRACTION39B329 - 339
40X-RAY DIFFRACTION40B340 - 356

+
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://pdbjlvh1.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