[English] 日本語
Yorodumi
- PDB-4b9q: Open conformation of ATP-bound Hsp70 homolog DnaK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b9q
TitleOpen conformation of ATP-bound Hsp70 homolog DnaK
ComponentsCHAPERONE PROTEIN DNAK
KeywordsCHAPERONE
Function / homology
Function and homology information


stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding ...stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / heat shock protein binding / inclusion body / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / DNA replication / protein-containing complex / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chaperone protein DnaK
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKopp, J. / Mayer, M.P. / Sinning, I.
CitationJournal: Mol.Cell / Year: 2012
Title: Structure and Dynamics of the ATP-Bound Open Conformation of Hsp70 Chaperones
Authors: Kityk, R. / Kopp, J. / Sinning, I. / Mayer, M.P.
History
DepositionSep 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHAPERONE PROTEIN DNAK
B: CHAPERONE PROTEIN DNAK
C: CHAPERONE PROTEIN DNAK
D: CHAPERONE PROTEIN DNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,20012
Polymers265,0744
Non-polymers2,1268
Water9,260514
1
A: CHAPERONE PROTEIN DNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8003
Polymers66,2681
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHAPERONE PROTEIN DNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8003
Polymers66,2681
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CHAPERONE PROTEIN DNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8003
Polymers66,2681
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CHAPERONE PROTEIN DNAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8003
Polymers66,2681
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.331, 77.470, 182.960
Angle α, β, γ (deg.)90.00, 101.71, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...
211CHAIN B AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...
311CHAIN C AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...
411CHAIN D AND (RESSEQ 2:180 OR RESSEQ 188:249 OR RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
2given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
3given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
4given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
5given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
6given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
7given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
8given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
9given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
10given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
11given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
12given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913
13given(0.998052, -0.024674, -0.057306), (-0.023967, 0.999628, -0.012989), (0.057605, -0.01159, -0.998272)185.667, -4.88265, 84.8367
14given(0.972173, 3.3E-5, -0.234264), (-0.001974, -0.999963, -0.008335), (-0.234256, 0.008565, -0.972137)22.9601, 137.01, 195.726
15given(0.983583, 0.042388, 0.175407), (-0.040773, -0.999086, 0.012805), (0.17579, 0.005443, 0.984413)179.639, 145.081, 71.2913

-
Components

#1: Protein
CHAPERONE PROTEIN DNAK / HSP70 / HEAT SHOCK 70 KDA PROTEIN / HEAT SHOCK PROTEIN 70


Mass: 66268.461 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PDMI.1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BB1553 / References: UniProt: P0A6Y8
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE
Crystal growTemperature: 291 K / pH: 7.6
Details: 28% PEG4000, 5% GLYCEROL, 0.1 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE PH 5.6, 5 MM ATP, 10 MM MGCL2, 291 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→59.72 Å / Num. obs: 108374 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 44.05 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.23
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.55 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1DKG AND 1DKX

1dkg

1dkx


Resolution: 2.4→59.717 Å / SU ML: 0.34 / σ(F): 0.46 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 5501 5.1 %
Rwork0.1964 --
obs0.1986 108315 99.54 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18118 0 128 514 18760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918473
X-RAY DIFFRACTIONf_angle_d1.09925008
X-RAY DIFFRACTIONf_dihedral_angle_d14.4797036
X-RAY DIFFRACTIONf_chiral_restr0.0662932
X-RAY DIFFRACTIONf_plane_restr0.0053284
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3603X-RAY DIFFRACTIONPOSITIONAL
12B3603X-RAY DIFFRACTIONPOSITIONAL0.048
13C3630X-RAY DIFFRACTIONPOSITIONAL0.047
14D3592X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.35541770.29423408X-RAY DIFFRACTION100
2.4273-2.45580.38831880.28363404X-RAY DIFFRACTION100
2.4558-2.48580.34621720.27743454X-RAY DIFFRACTION100
2.4858-2.51720.33261740.2633433X-RAY DIFFRACTION100
2.5172-2.55040.32591820.25113392X-RAY DIFFRACTION100
2.5504-2.58530.32261780.23673465X-RAY DIFFRACTION100
2.5853-2.62220.27091970.23863330X-RAY DIFFRACTION100
2.6222-2.66140.29591970.23113456X-RAY DIFFRACTION100
2.6614-2.7030.29391760.22723425X-RAY DIFFRACTION100
2.703-2.74730.30381960.22593367X-RAY DIFFRACTION100
2.7473-2.79470.29671770.2313443X-RAY DIFFRACTION100
2.7947-2.84550.32371730.22713462X-RAY DIFFRACTION100
2.8455-2.90020.26761850.21773419X-RAY DIFFRACTION100
2.9002-2.95940.27551710.21633429X-RAY DIFFRACTION100
2.9594-3.02370.30441950.21343404X-RAY DIFFRACTION100
3.0237-3.09410.25741900.20663463X-RAY DIFFRACTION100
3.0941-3.17150.28831890.2193387X-RAY DIFFRACTION100
3.1715-3.25720.25171790.21443434X-RAY DIFFRACTION100
3.2572-3.3530.26121830.20713452X-RAY DIFFRACTION100
3.353-3.46120.25581800.20153405X-RAY DIFFRACTION100
3.4612-3.58490.25111970.19443444X-RAY DIFFRACTION100
3.5849-3.72850.20091720.17963424X-RAY DIFFRACTION100
3.7285-3.89810.19841740.17243451X-RAY DIFFRACTION99
3.8981-4.10360.19911710.17913426X-RAY DIFFRACTION99
4.1036-4.36060.1911810.16273435X-RAY DIFFRACTION99
4.3606-4.69720.21141830.15813426X-RAY DIFFRACTION99
4.6972-5.16960.22871780.16353450X-RAY DIFFRACTION99
5.1696-5.91710.19022060.17513430X-RAY DIFFRACTION99
5.9171-7.45270.20941800.19843457X-RAY DIFFRACTION99
7.4527-59.73520.18612000.18323439X-RAY DIFFRACTION96
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)
14.34590.67760.98654.3385-0.59374.28350.05860.1402-0.2965-0.3266-0.1079-0.31640.02590.21650.01250.26280.01430.03980.23670.03790.3025110.669888.230594.7495
21.6261-2.09660.72216.7162-0.2671.65980.2203-0.18460.01960.086-0.0508-0.57810.32510.0394-0.08160.3607-0.0769-0.03220.33770.05430.461109.333971.4801105.6626
33.68882.10231.80865.34931.64394.35920.0215-0.74450.6661.0369-0.23970.3332-1.0685-0.26690.19760.9275-0.01260.07370.564-0.09130.4703104.1098102.4207118.5543
40.7777-1.0273-1.6323.16755.18037.02650.11640.01050.1452-0.05590.1924-0.2182-0.22520.2089-0.21070.7630.03560.10460.3090.09230.4472117.050788.871662.5122
52.3874-0.0717-0.82122.76410.40494.44750.0184-0.21060.04620.30130.0696-0.1556-0.27190.0307-0.07030.39680.0048-0.09190.26090.00270.284377.729293.034-10.4931
65.23623.0474-2.12714.9607-2.05653.95870.2661-0.1435-0.07210.44220.0870.27830.3381-0.3129-0.30450.5537-0.006-0.09110.3065-0.02090.310669.065473.7461-16.2569
71.2768-0.34590.08182.1475-0.50253.47380.0002-0.04410.26330.26960.18530.0703-0.9765-0.3156-0.19880.65060.038-0.03810.3144-0.03980.471974.8025102.6871-5.7686
82.7519-0.14270.80856.4842-1.5383.58520.1987-0.05550.23180.974-0.12060.158-0.18870.12110.03110.4670.01870.11680.23490.05770.3753105.24549.303876.1255
91.04032.9578-0.82878.5377-1.51751.74310.3127-0.1553-0.18540.683-0.1703-0.365-0.45780.0491-0.12690.51310.09010.05220.32210.09990.5013110.307467.452667.1816
101.5219-0.07640.73043.49772.02594.2320.48760.3247-0.2720.08620.0994-0.0590.94460.4677-0.55350.38480.00470.04240.23160.14590.5163107.315539.485378.446
113.3511-0.4233-0.24343.71730.23615.59260.04390.14290.2661-0.4110.195-0.3775-0.097-0.2491-0.24220.4568-0.02680.00680.2394-0.02340.42174.284554.001910.26
120.792-1.37980.50275.20880.02692.31790.0987-0.25810.06870.23040.2355-0.6216-0.24330.0574-0.29070.4932-0.0927-0.04090.4228-0.03330.544680.186764.864122.9771
131.5208-0.5271.64551.3237-1.2444.91560.1826-0.0785-0.2276-0.15070.1167-0.02930.9963-0.2279-0.31610.6505-0.0711-0.10350.3517-0.02350.494170.272646.64730.7094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 163 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 164 THROUGH 369 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 370 THROUGH 508 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 509 THROUGH 602 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 2 THROUGH 228 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 229 THROUGH 369 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 370 THROUGH 605 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 2 THROUGH 213 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 214 THROUGH 369 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 370 THROUGH 603 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 2 THROUGH 163 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 164 THROUGH 435 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 436 THROUGH 605 )

+
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