[English] 日本語
Yorodumi
- PDB-3pcs: Structure of EspG-PAK2 autoinhibitory Ialpha3 helix complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pcs
TitleStructure of EspG-PAK2 autoinhibitory Ialpha3 helix complex
Components
  • EspG
  • Serine/threonine-protein kinase PAK 2
KeywordsPROTEIN TRANSPORT/TRANSFERASE / BACTERIAL EFFECTOR / KINASE / AUTOINHIBITORY IALPHA3 HELIX / PROTEIN TRANSPORT-TRANSFERASE complex
Function / homology
Function and homology information


Regulation of PAK-2p34 activity by PS-GAP/RHG10 / negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / virus-mediated perturbation of host defense response => GO:0019049 / signal transduction => GO:0007165 / small GTPase binding => GO:0031267 / protein localization to cell-cell junction / Stimulation of the cell death response by PAK-2p34 / dendritic spine development / bicellular tight junction assembly / adherens junction assembly ...Regulation of PAK-2p34 activity by PS-GAP/RHG10 / negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / virus-mediated perturbation of host defense response => GO:0019049 / signal transduction => GO:0007165 / small GTPase binding => GO:0031267 / protein localization to cell-cell junction / Stimulation of the cell death response by PAK-2p34 / dendritic spine development / bicellular tight junction assembly / adherens junction assembly / Nef and signal transduction / interleukin-12-mediated signaling pathway / Activation of RAC1 / positive regulation of extrinsic apoptotic signaling pathway / regulation of growth / CD28 dependent Vav1 pathway / Ephrin signaling / negative regulation of stress fiber assembly / regulation of cytoskeleton organization / regulation of axonogenesis / stress-activated protein kinase signaling cascade / protein tyrosine kinase activator activity / activation of protein kinase activity / RHO GTPases activate PAKs / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Sema3A PAK dependent Axon repulsion / Generation of second messenger molecules / cellular response to organic cyclic compound / Smooth Muscle Contraction / vascular endothelial growth factor receptor signaling pathway / T cell costimulation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / CD209 (DC-SIGN) signaling / Regulation of activated PAK-2p34 by proteasome mediated degradation / VEGFR2 mediated vascular permeability / FCERI mediated MAPK activation / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / small GTPase binding / VEGFA-VEGFR2 Pathway / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / T cell receptor signaling pathway / peptidyl-serine phosphorylation / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / cysteine-type endopeptidase activity / phosphorylation / protein phosphorylation / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / signal transduction / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21-activated kinase 2, catalytic domain / Serine/threonine-protein kinase PAK2 / EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. ...p21-activated kinase 2, catalytic domain / Serine/threonine-protein kinase PAK2 / EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 2 / T3SS secreted effector EspG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.86 Å
AuthorsTomchick, D.R. / Alto, N.M. / Selyunin, A.S.
CitationJournal: Nature / Year: 2011
Title: The assembly of a GTPase-kinase signalling complex by a bacterial catalytic scaffold.
Authors: Selyunin, A.S. / Sutton, S.E. / Weigele, B.A. / Reddick, L.E. / Orchard, R.C. / Bresson, S.M. / Tomchick, D.R. / Alto, N.M.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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: EspG
B: EspG
C: EspG
D: EspG
E: Serine/threonine-protein kinase PAK 2
F: Serine/threonine-protein kinase PAK 2
G: Serine/threonine-protein kinase PAK 2
H: Serine/threonine-protein kinase PAK 2


Theoretical massNumber of molelcules
Total (without water)165,8148
Polymers165,8148
Non-polymers00
Water0
1
A: EspG
E: Serine/threonine-protein kinase PAK 2


Theoretical massNumber of molelcules
Total (without water)41,4542
Polymers41,4542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area17100 Å2
MethodPISA
2
B: EspG
F: Serine/threonine-protein kinase PAK 2


Theoretical massNumber of molelcules
Total (without water)41,4542
Polymers41,4542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area17110 Å2
MethodPISA
3
C: EspG
G: Serine/threonine-protein kinase PAK 2


Theoretical massNumber of molelcules
Total (without water)41,4542
Polymers41,4542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area16480 Å2
MethodPISA
4
D: EspG
H: Serine/threonine-protein kinase PAK 2


Theoretical massNumber of molelcules
Total (without water)41,4542
Polymers41,4542
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.717, 104.603, 191.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
EspG / EspG protein


Mass: 39611.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs4590, espG, Z5142 / Plasmid: pPRO-EX-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DB50
#2: Protein/peptide
Serine/threonine-protein kinase PAK 2 / Gamma-PAK / PAK65 / S6/H4 kinase / p21-activated kinase 2 / PAK-2 / p58 / PAK-2p27 / p27 / PAK-2p34 ...Gamma-PAK / PAK65 / S6/H4 kinase / p21-activated kinase 2 / PAK-2 / p58 / PAK-2p27 / p27 / PAK-2p34 / p34 / C-t-PAK2


Mass: 1842.097 Da / Num. of mol.: 4 / Fragment: UNP residues 121-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK2 / Plasmid: pGEX-4TI1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13177, non-specific serine/threonine protein kinase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG 4000, 0.25 M NaCl, 0.1 M Tris pH 8.0, 15% ethylene glycol, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 16, 2009 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 44259 / Num. obs: 44259 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.854.70.681199.5
2.85-2.94.80.5951100
2.9-2.964.90.5241100
2.96-3.024.90.4321100
3.02-3.084.90.3381100
3.08-3.154.90.2521100
3.15-3.234.90.2271100
3.23-3.324.90.1821100
3.32-3.424.90.1511100
3.42-3.534.90.117199.9
3.53-3.654.90.0921100
3.65-3.84.80.0821100
3.8-3.974.80.0781100
3.97-4.184.80.063199.9
4.18-4.444.80.0521100
4.44-4.794.80.051100
4.79-5.274.70.051199.8
5.27-6.034.60.053199.9
6.03-7.594.40.045199.8
7.59-504.40.032198.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
DMphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PCR

3pcr


Resolution: 2.86→40.5 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 2032 4.95 %
Rwork0.191 --
obs0.195 41057 99.9 %
all-41057 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.44 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 76.93 Å2
Baniso -1Baniso -2Baniso -3
1-6.0681 Å2-0 Å20 Å2
2---12.5068 Å2-0 Å2
3---6.4387 Å2
Refine analyzeLuzzati sigma a obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.86→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11254 0 0 0 11254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811452
X-RAY DIFFRACTIONf_angle_d1.21615534
X-RAY DIFFRACTIONf_dihedral_angle_d14.5034283
X-RAY DIFFRACTIONf_chiral_restr0.0791802
X-RAY DIFFRACTIONf_plane_restr0.0052026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.96210.40382330.31773822X-RAY DIFFRACTION100
2.9621-3.08060.36272110.28313851X-RAY DIFFRACTION100
3.0806-3.22070.37781940.24133848X-RAY DIFFRACTION100
3.2207-3.39020.33751810.24353885X-RAY DIFFRACTION100
3.3902-3.60230.31241840.22463881X-RAY DIFFRACTION100
3.6023-3.87990.28161950.19853884X-RAY DIFFRACTION100
3.8799-4.26930.24912140.17113874X-RAY DIFFRACTION100
4.2693-4.88470.21471920.13623931X-RAY DIFFRACTION100
4.8847-6.14510.27341970.17863972X-RAY DIFFRACTION100
6.1451-29.59760.25432310.16534077X-RAY DIFFRACTION99
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)
10.5938-0.5151-0.13631.82440.85670.45630.1620.13420.041-0.00330.1053-0.57890.37390.2272-0.21320.2640.0702-0.07160.16780.01440.3318-30.2629-23.99851.5692
21.7048-2.11190.2719.71141.37530.47650.43460.1841-0.1213-1.7821-0.4157-0.29-0.1782-0.2304-0.010.4630.07190.01440.2548-0.08950.2687-39.7034-27.9782-3.9012
32.27762.1184-0.29592.34440.63062.5460.0088-0.04710.72630.29790.02880.49740.11720.3377-0.17140.14920.09580.00150.2003-0.02280.2884-42.3417-19.953610.6947
41.72430.995-0.30051.1831-0.4821.5812-0.1235-0.26170.4091-0.0145-0.03790.1259-0.3365-0.07820.05480.11090.0372-0.03110.0825-0.00410.2403-34.3369-0.5896-0.0387
58.4012-6.01882.07445.0885-1.45840.5232-0.87450.14112.53391.6287-0.1132-0.5371-0.27080.2460.57021.07180.04060.0560.28680.25440.7587-34.577912.8635-13.5612
61.303-0.55220.6012.6122-0.03271.08080.00230.4950.3598-0.7036-0.41970.1385-0.0801-0.29750.02850.2255-0.01060.02590.20460.110.0092-34.7328-2.595-12.9733
70.99930.42390.49982.3780.65922.37460.17710.081-0.01280.0213-0.1906-0.0120.3107-0.0920.10020.11250.01120.04090.09290.05360.108-37.7131-2.26886.5819
81.31340.030.30824.088-0.58460.47620.18070.0449-0.5102-1.03160.0586-0.0680.0056-0.0639-0.17740.4763-0.08270.05450.2570.0480.2978-73.4257-3.84712.2475
9-0.01530.2844-0.10053.2615-0.23792.24840.04630.03020.112-0.0891-0.60970.30590.5929-0.18110.38050.5037-0.0804-0.02080.191-0.04120.3028-81.238-9.66657.0136
103.41030.3098-1.58033.76853.00235.51950.49150.24460.06390.07360.4678-0.51080.2671-0.0243-0.42460.2891-0.0761-0.10210.31380.03340.2852-73.77341.364617.7558
111.9697-0.8648-0.82650.63180.21781.03860.22870.04360.6273-0.80020.1028-0.0692-0.7913-0.085-0.22660.5894-0.11580.01630.12870.00890.4808-77.126618.27437.3335
121.7204-0.35060.33640.58491.0862.9943-0.59790.08890.3347-0.9574-0.1844-1.06121.4876-0.31670.46310.8949-0.0564-0.0290.07580.05541.1353-89.286532.58450.6825
130.2098-0.30290.14733.05020.55090.97050.21390.09210.2612-1.00460.15910.2709-0.84820.0407-0.20650.6514-0.0144-0.10460.30240.10250.4573-87.727317.5246-1.7584
141.4025-0.24230.16953.60560.6230.75650.24030.02350.0431-0.49240.0727-0.1468-0.13830.0613-0.19610.3346-0.0982-0.02970.18950.01170.2721-75.600716.252713.9137
152.07221.7376-0.34162.3608-0.58591.19730.0988-0.6857-0.0895-0.0914-0.20620.00550.10410.30120.09870.0786-0.0168-0.0970.3122-0.0510.25-99.71190.84247.6536
168.39485.5742-8.21416.5893-7.38139.81830.3236-1.0378-1.0565-0.7642-0.5243-0.2580.44151.67720.32190.33490.00820.01860.31830.09960.4375-97.9172-9.086141.6496
171.8341-0.3558-2.19391.75270.09012.81020.0767-0.76361.03760.23650.00810.304-0.67160.1960.02710.4090.0247-0.07940.23710.05190.3101-95.80864.337133.8331
181.7306-0.8699-0.05281.189-0.25950.5638-0.159-0.16130.45630.14050.1456-0.2619-0.46160.01560.03180.2845-0.1942-0.15210.4257-0.05860.4367-78.969410.929446.8786
192.3017-1.3213-0.13171.30350.02440.89910.0035-0.913-0.4162-0.13750.68030.1652-0.0512-0.5676-0.63990.5503-0.1944-0.54981.0880.05250.8161-60.72726.488557.1253
203.01330.6160.41411.4998-1.04992.5002-0.0812-0.7146-0.32620.3371-0.1587-0.69090.1510.36760.19850.3477-0.043-0.29450.57980.09020.4004-74.74680.062855.0546
215.13890.82590.97091.15240.61332.80050.0335-0.36580.6582-0.0768-0.1486-0.5152-0.50670.33710.15820.3076-0.1475-0.06290.40010.00970.431-79.808412.008841.2318
223.34242.22930.27881.83520.57361.25110.0267-0.2615-0.274-0.1089-0.08240.01910.1904-0.2890.07720.30730.0574-0.11610.4572-0.05050.4154-32.3842-13.21344.6432
237.37715.70441.39336.2655-2.91038.9399-0.0940.308-2.02-0.4380.6262-1.88571.36990.64210.3489-0.0875-0.08480.03410.23010.03170.6417-22.2772-17.222940.4318
241.27830.7590.12166.88082.69644.26581.0827-0.8811-0.58770.95430.0373-0.96140.40470.3593-0.64090.8311-0.2707-0.17051.0838-0.00280.6714-29.1354-26.548252.988
255.413-2.7428-1.09553.5336-0.44764.2685-0.5815-0.8969-2.29551.35020.20160.97971.75670.8975-0.1969-0.1372-0.3696-0.3051-0.11430.0338-0.0586-43.6963-26.546850.1571
261.7568-3.1833-1.47938.4092.79322.1668-0.3427-0.2421-0.78121.0360.34290.83960.4981-0.2110.03910.2129-0.1373-0.00470.46340.25560.3712-50.5822-34.182431.1126
271.7123-1.1256-2.02951.51960.89622.94330.4201-0.2640.3614-0.07150.0880.08140.08460.1495-0.37260.1234-0.0612-0.08020.0885-0.0120.199-44.7082-26.370424.4933
283.1404-0.02220.60862.8508-0.93652.11030.081-0.6424-0.46230.6236-0.0725-0.00390.25560.1699-0.13240.295-0.0734-0.14420.2360.14570.224-44.8547-34.112944.8855
291.9767-3.2213-1.01885.78432.32071.3358-0.44220.5735-0.57862.4508-0.1428-1.60561.0776-0.37690.71991.1141-0.1235-0.03060.57440.13150.9281-40.545510.031910.2038
302.70432.2828-0.16566.6119-4.32493.74160.57360.02131.2838-0.5392-0.30770.2597-1.2077-0.3396-0.05820.6368-0.2003-0.20660.4811-0.03770.714-33.1668.30139.2102
317.8851.2157-6.10930.3633-0.99074.8528-0.57490.12411.44230.70891.09641.0246-1.12080.36930.10021.0630.08520.08330.29810.2710.7472-21.68365.97791.7618
326.33140.4203-1.94066.68682.19778.40570.478-0.20330.4487-0.17431.1108-0.05510.1639-0.4718-0.94320.58490.1591-0.02210.62180.01160.9452-74.786127.933520.0423
331.92822.28151.38223.3262.48362.76920.88020.4484-0.5818-1.32980.8088-2.0359-1.5106-0.921-1.28931.0980.00870.28460.58390.17940.8974-70.719326.18667.3684
344.12891.0462-2.49430.5709-1.19582.99340.1856-0.07830.475-1.79020.158-0.58180.5152-0.1747-0.22471.3098-0.2769-0.17340.75880.16891.8431-71.418322.182540.2354
352.0913-1.71113.45474.4-2.33615.7646-0.29240.09330.08090.6631-0.8601-1.248-0.4422-0.07880.92740.7218-0.2866-0.28811.04590.29351.5967-76.591120.706650.9512
361.55452.23341.97333.33961.83849.1009-0.08932.4535-0.36460.63070.5785-0.55871.5097-1.1582-0.05010.673-0.2073-0.34141.00020.20270.8028-53.7848-43.883346.2171
370.2406-0.68511.05232.8891-3.71338.24740.1558-0.30360.4522-0.43210.24980.49920.05790.1095-0.15520.7115-0.4858-0.26851.26050.41910.5814-55.6048-35.862846.0971
383.29782.2603-0.39425.9624-4.76325.2131.46320.51040.67171.6014-0.3291.23090.2311-1.0793-1.46990.7201-0.1739-0.06420.5710.31481.235-60.478-26.44139.476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 42:103)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 104:129)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 130:156)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 157:234)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 235:245)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 246:301)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 302:397)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 44:105)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 106:136)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 137:156)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 157:234)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 235:245)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 246:301)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 302:397)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 42:105)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 106:131)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 132:149)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 150:236)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 237:246)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 247:301)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 302:395)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 42:105)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 106:131)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 132:151)
25X-RAY DIFFRACTION25(CHAIN D AND RESID 152:186)
26X-RAY DIFFRACTION26(CHAIN D AND RESID 187:245)
27X-RAY DIFFRACTION27(CHAIN D AND RESID 246:296)
28X-RAY DIFFRACTION28(CHAIN D AND RESID 297:395)
29X-RAY DIFFRACTION29(CHAIN E AND RESID 122:124)
30X-RAY DIFFRACTION30(CHAIN E AND RESID 125:129)
31X-RAY DIFFRACTION31(CHAIN E AND RESID 130:134)
32X-RAY DIFFRACTION32(CHAIN F AND RESID 122:126)
33X-RAY DIFFRACTION33(CHAIN F AND RESID 127:132)
34X-RAY DIFFRACTION34(CHAIN G AND RESID 123:126)
35X-RAY DIFFRACTION35(CHAIN G AND RESID 127:131)
36X-RAY DIFFRACTION36(CHAIN H AND RESID 122:125)
37X-RAY DIFFRACTION37(CHAIN H AND RESID 126:129)
38X-RAY DIFFRACTION38(CHAIN H AND RESID 130:133)

+
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