[English] 日本語
Yorodumi
- PDB-4xgc: Crystal structure of the eukaryotic origin recognition complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xgc
TitleCrystal structure of the eukaryotic origin recognition complex
Components(Origin recognition complex subunit ...) x 7
KeywordsDNA BINDING PROTEIN / protein complex
Function / homology
Function and homology information


alpha-heterochromatin / CDC6 association with the ORC:origin complex / larval feeding behavior / septin cytoskeleton / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification ...alpha-heterochromatin / CDC6 association with the ORC:origin complex / larval feeding behavior / septin cytoskeleton / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / origin recognition complex / positive regulation of border follicle cell migration / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / olfactory learning / nuclear pre-replicative complex / DNA replication preinitiation complex / mitotic chromosome condensation / mitotic DNA replication checkpoint signaling / chromosome condensation / DNA replication origin binding / DNA replication initiation / nuclear pore / ribonucleoprotein complex binding / heterochromatin / GTPase activator activity / mitotic spindle organization / learning / DNA-templated DNA replication / mitotic cell cycle / learning or memory / DNA replication / chromatin binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Cdc6, C-terminal / CDC6, C terminal winged helix domain ...Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Cdc6, C-terminal / CDC6, C terminal winged helix domain / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 3, N-terminal / : / : / Origin recognition complex (ORC) subunit 3 N-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex winged helix C-terminal / ORC5, lid domain / Orc1-like, AAA ATPase domain / : / : / Origin recognition complex subunit 2 RecA-like domain / ORC2 WHD / AAA ATPase domain / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Origin recognition complex subunit 1 / Origin recognition complex subunit 2 / Origin recognition complex subunit 5 / Origin recognition complex subunit 3 / Origin recognition complex subunit 4 / Origin recognition complex subunit 6
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsBleichert, F. / Botchan, M.R. / Berger, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071747 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA R37-30490 United States
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the eukaryotic origin recognition complex.
Authors: Bleichert, F. / Botchan, M.R. / Berger, J.M.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Origin recognition complex subunit 2
C: Origin recognition complex subunit 3
E: Origin recognition complex subunit 5
A: Origin recognition complex subunit 1
G: Origin recognition complex subunit 2
F: Origin recognition complex subunit 6
D: Origin recognition complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,6349
Polymers277,5597
Non-polymers752
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24310 Å2
ΔGint-127 kcal/mol
Surface area90360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.545, 258.983, 257.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
DetailsThe depositor states that the biological assembly is hexameric, not heptameric. Orc2 was deposited as 2 different chains because the N-terminus could only be built as a discontinuous polyalanine model. However, both chains belong to the same polypeptide.

-
Components

-
Origin recognition complex subunit ... , 7 types, 7 molecules BCEAGFD

#1: Protein Origin recognition complex subunit 2 / DmORC2


Mass: 40106.762 Da / Num. of mol.: 1 / Fragment: residues 266-618
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc2, CG3041 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q24168
#2: Protein Origin recognition complex subunit 3 / FI24229p1 / GH28787p / LP02234p1 / Latheo


Mass: 77650.078 Da / Num. of mol.: 1 / Fragment: residues 47-721
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: lat, CG34315-RB, lat-RA, CG4088, Dmel_CG4088 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7K2L1
#3: Protein Origin recognition complex subunit 5


Mass: 52175.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc5, CG7833 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q24169
#4: Protein Origin recognition complex subunit 1 / DmORC1


Mass: 43910.801 Da / Num. of mol.: 1 / Fragment: residues 533-924
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc1, CG10667 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O16810
#5: Protein/peptide Origin recognition complex subunit 2


Mass: 3507.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc2, CG3041 / Production host: Trichoplusia ni (cabbage looper)
#6: Protein Origin recognition complex subunit 6


Mass: 8204.343 Da / Num. of mol.: 1 / Fragment: residues 187-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc6, CG1584 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y1B2
#7: Protein Origin recognition complex subunit 4 / LD43280p


Mass: 52004.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Orc4, CG2917, Dmel_CG2917 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9W102, nucleoside-triphosphate phosphatase

-
Non-polymers , 2 types, 2 molecules

#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

-
Details

Has protein modificationN
Sequence detailsTHE AUTHOR STATES THAT CHAIN G IS LIKELY PART OF THE N-TERMINUS OF CHAIN B. 61 N-TERMINAL RESIDUES ...THE AUTHOR STATES THAT CHAIN G IS LIKELY PART OF THE N-TERMINUS OF CHAIN B. 61 N-TERMINAL RESIDUES ARE MISSING (DISORDERED). OWING TO LOW RESOLUTION, IT WAS NOT POSSIBLE TO ACCURATELY ASSIGN THE SIDE CHAINS AND IDENTIFY THE PEPTIDE. THE N-TERMINUS WAS MODELED AS ALA, BUT THE SEQUENCE ALIGNMENT IS UNKNOWN, AND WAS THEREFORE CHANGED TO UNK IN THIS ENTRY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: PIPES (pH 7.5), magnesium chloride, ammonium acetate, PEG 20000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332, 1.71083
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.710831
ReflectionResolution: 3.5→48.8 Å / Num. obs: 61418 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 118.6 Å2 / Rmerge(I) obs: 0.214 / Net I/σ(I): 7.7
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 8.6 % / Rmerge(I) obs: 2.181 / Mean I/σ(I) obs: 1.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
Aimlessdata scaling
XDSdata scaling
SHELXphasing
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: SAD SOLUTION

Resolution: 3.5→48.799 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / Phase error: 28.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 1738 2.83 %random selection
Rwork0.2243 ---
obs0.2253 61399 99.96 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.1 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16336 0 2 0 16338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d016615
X-RAY DIFFRACTIONf_angle_d0.722442
X-RAY DIFFRACTIONf_dihedral_angle_d11.616151
X-RAY DIFFRACTIONf_chiral_restr0.022613
X-RAY DIFFRACTIONf_plane_restr02854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.6030.35721370.30094921X-RAY DIFFRACTION100
3.603-3.71920.33571470.29734904X-RAY DIFFRACTION100
3.7192-3.85210.34091460.28134929X-RAY DIFFRACTION100
3.8521-4.00630.28691420.25694940X-RAY DIFFRACTION100
4.0063-4.18850.29481430.22374938X-RAY DIFFRACTION100
4.1885-4.40920.24791440.20284920X-RAY DIFFRACTION100
4.4092-4.68520.20771430.18824965X-RAY DIFFRACTION100
4.6852-5.04670.25191460.18554944X-RAY DIFFRACTION100
5.0467-5.55390.23821450.20734964X-RAY DIFFRACTION100
5.5539-6.3560.27331460.24565018X-RAY DIFFRACTION100
6.356-8.00220.25681440.24665017X-RAY DIFFRACTION100
8.0022-48.80320.23171550.20795201X-RAY DIFFRACTION100
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)
10.7696-0.31850.06360.12770.5074-0.0763-0.0694-0.0740.12370.27190.01860.49370.21940.2333-00.9150.09390.20390.613-0.05470.7063-13.1297-72.977683.1367
2-0.8018-0.9272-0.20670.9771-0.41140.12620.0931-0.36190.04790.0822-0.01650.01230.06350.030600.58780.03030.08531.0142-0.16750.52266.9548-98.775470.4728
3-0.3376-0.269-0.4915-0.1729-0.0838-0.07331.1728-1.64681.5454-0.6579-0.95551.0890.2427-0.270800.8540.5791-0.2429-0.1120.17920.3505-17.3471-48.11966.8204
40.06990.2692-0.53530.34630.59330.25070.1347-0.1701-0.1999-0.17550.15910.1767-0.1078-0.5501-00.33930.15810.09330.2448-0.12850.3536-10.4004-64.642949.5538
50.34810.0285-0.0746-0.5043-0.27260.7396-0.0962-0.2450.221-0.13080.1468-0.1810.1010.270500.68590.07220.14090.6179-0.19560.8937-13.2308-44.54984.8702
6-0.09620.5792-0.6353-0.03870.241-0.3071-0.5270.10430.7641-0.27871.1364-0.38230.485-1.549-00.48770.18820.3116-0.081-0.47581.2677-6.9316-25.363984.6506
7-0.2464-0.0707-0.61020.21830.07580.05-0.65010.03150.7790.53680.83430.55350.50490.70201.35850.688-0.01390.9946-0.55340.477610.0431-77.056696.5182
81.2489-0.7564-0.4460.8278-0.61240.83570.00230.02670.03610.09090.00980.0902-0.125-0.0684-00.4198-0.0324-0.07820.4378-0.04440.404-2.2493-84.502127.4491
9-0.6989-0.9573-0.0179-0.02260.0811-0.6472-0.00830.159-0.44450.13610.3549-0.82180.2698-0.0548-00.4891-0.08830.16440.45590.07430.247412.7842-61.354224.8386
10-0.3938-0.2693-1.00310.4036-0.0527-0.02680.0701-0.41580.5287-0.06590.22810.05510.27410.157400.8039-0.0084-0.07440.5249-0.13230.930614.3641-50.891443.8185
110.1909-0.00430.56060.3024-0.17310.03820.0461-0.29850.3008-0.08110.14-0.0053-0.02270.170500.54760.1925-0.01240.7521-0.31990.914616.5152-62.744273.6894
120.80270.20940.04910.0249-0.71480.09010.1399-0.5030.1495-0.0731-0.077-0.076-0.10170.1561-00.82790.0255-0.22131.2163-0.11690.763238.1996-100.300571.6497
130.2212-0.56580.50490.3617-0.48550.7221-0.0049-0.0677-0.0477-0.15310.0618-0.0286-0.04910.0214-00.26960.0298-0.03910.4299-0.08760.434830.3475-111.804444.9313
14-0.0957-0.2106-0.1039-0.13610.1311-0.25570.02740.58240.6667-0.44230.38470.2404-0.39511.347401.42650.3314-0.01371.5946-0.17870.818420.6203-68.425989.4486
150.03790.073-0.01320.183-0.01520.00510.10310.03090.2663-0.04590.013-0.1066-0.2924-0.1162-0.00021.26690.4233-0.47771.9281-1.0612.260225.4799-88.629796.3783
160.07950.01120.01150.02140.01850.00120.00130.1904-0.1410.00020.23450.6250.035-0.0005-0.00021.4631.1262-0.03290.3604-1.10092.381613.8138-96.89897.8256
170.0111-0.0169-0.01830.05150.03360.03360.3052-0.1048-0.1321-0.1366-0.1558-0.01230.09910.0357-01.3534-0.1732-0.0731.27160.61211.51640.5482-95.083101.2803
180.0127-0.10490.0848-0.02130.0233-0.0031-0.4761-0.6458-0.2582-0.3695-0.1810.0350.5074-0.6827-02.7105-0.0047-0.42441.5161-0.10121.1358-18.2306-37.4867118.0357
19-0.1552-0.6513-0.12580.285-0.38570.4198-0.13570.083-0.0826-0.02220.01130.16710.0509-0.065500.403-0.04370.02670.5088-0.07330.4211-5.5615-111.407630.7194
200.1987-0.4270.42710.17180.0396-0.1474-0.0366-0.0366-0.10240.2243-0.0253-0.06590.05260.1307-00.4963-0.06410.00330.50890.01640.437-2.8364-114.455745.4559
21-0.3931-0.4898-0.355-0.0309-0.69160.24290.00820.1576-0.0610.13910.08660.0385-0.10070.061700.466-0.02520.05360.5195-0.02030.43193.2758-110.192619.6847
220.6142-0.3712-0.0340.3574-0.46540.06910.04550.2420.30550.0646-0.0796-0.02720.24840.163900.40580.0099-0.00940.7319-0.06690.430317.7694-97.605813.9105
230.2656-0.00170.37240.5809-0.65240.66720.0349-0.0195-0.09770.1478-0.1011-0.2852-0.0614-0.142400.5247-0.0521-0.06050.4898-0.07170.566227.0648-71.054442.335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 326 through 497 )
2X-RAY DIFFRACTION2chain 'B' and (resid 498 through 616 )
3X-RAY DIFFRACTION3chain 'C' and (resid 46 through 88 )
4X-RAY DIFFRACTION4chain 'C' and (resid 89 through 252 )
5X-RAY DIFFRACTION5chain 'C' and (resid 253 through 381 )
6X-RAY DIFFRACTION6chain 'C' and (resid 382 through 598 )
7X-RAY DIFFRACTION7chain 'C' and (resid 599 through 721 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 159 )
9X-RAY DIFFRACTION9chain 'E' and (resid 160 through 243 )
10X-RAY DIFFRACTION10chain 'E' and (resid 244 through 337 )
11X-RAY DIFFRACTION11chain 'E' and (resid 338 through 458 )
12X-RAY DIFFRACTION12chain 'A' and (resid 569 through 737 )
13X-RAY DIFFRACTION13chain 'A' and (resid 738 through 919 )
14X-RAY DIFFRACTION14chain 'G' and (resid 1 through 19 )
15X-RAY DIFFRACTION15chain 'G' and (resid 20 through 24 )
16X-RAY DIFFRACTION16chain 'G' and (resid 25 through 34 )
17X-RAY DIFFRACTION17chain 'G' and (resid 35 through 41 )
18X-RAY DIFFRACTION18chain 'F' and (resid 223 through 241 )
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 132 )
20X-RAY DIFFRACTION20chain 'D' and (resid 133 through 197 )
21X-RAY DIFFRACTION21chain 'D' and (resid 198 through 264 )
22X-RAY DIFFRACTION22chain 'D' and (resid 265 through 332 )
23X-RAY DIFFRACTION23chain 'D' and (resid 333 through 457 )

+
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