[English] 日本語
Yorodumi
- PDB-3sja: Crystal structure of S. cerevisiae Get3 in the open state in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sja
TitleCrystal structure of S. cerevisiae Get3 in the open state in complex with Get1 cytosolic domain
Components
  • ATPase GET3
  • Golgi to ER traffic protein 1
KeywordsHYDROLASE/TRANSPORT PROTEIN / Coiled-coil / receptor complex / TA-protein biogenesis / GET pathway / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum membrane / GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion ...establishment of protein localization to endoplasmic reticulum membrane / GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein transmembrane transporter activity / mitophagy / protein-membrane adaptor activity / protein folding chaperone / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / cellular response to oxidative stress / response to heat / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Get 1, fungi / Helix hairpin bin / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / Helix Hairpins ...Get 1, fungi / Helix hairpin bin / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Golgi to ER traffic protein 1 / ATPase GET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsReitz, S. / Wild, K. / Sinning, I.
CitationJournal: Science / Year: 2011
Title: Structural basis for tail-anchored membrane protein biogenesis by the Get3-receptor complex.
Authors: Stefer, S. / Reitz, S. / Wang, F. / Wild, K. / Pang, Y.Y. / Schwarz, D. / Bomke, J. / Hein, C. / Lohr, F. / Bernhard, F. / Denic, V. / Dotsch, V. / Sinning, I.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3May 14, 2014Group: Refinement description
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: ATPase GET3
B: ATPase GET3
C: Golgi to ER traffic protein 1
D: Golgi to ER traffic protein 1
E: ATPase GET3
F: ATPase GET3
G: Golgi to ER traffic protein 1
H: Golgi to ER traffic protein 1
I: ATPase GET3
J: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,66820
Polymers241,80710
Non-polymers86110
Water905
1
A: ATPase GET3
B: ATPase GET3
C: Golgi to ER traffic protein 1
D: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1689
Polymers96,7234
Non-polymers4455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-93 kcal/mol
Surface area38980 Å2
MethodPISA
2
E: ATPase GET3
F: ATPase GET3
G: Golgi to ER traffic protein 1
H: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9787
Polymers96,7234
Non-polymers2553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-77 kcal/mol
Surface area39400 Å2
MethodPISA
3
I: ATPase GET3
J: Golgi to ER traffic protein 1
hetero molecules

I: ATPase GET3
J: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0448
Polymers96,7234
Non-polymers3214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6230 Å2
ΔGint-90 kcal/mol
Surface area39590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.120, 91.460, 149.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11I-363-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
33
43
53

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain F and (resseq 5:105 or resseq 116:280 or resseq 285:353 )
211chain I and (resseq 5:105 or resseq 116:280 or resseq 285:353 )
112chain B and (resseq 5:105 or resseq 117:280 or resseq 285:353 )
212chain E and (resseq 5:105 or resseq 117:280 or resseq 285:353 )
113chain C and (resseq 18:78 )
213chain D and (resseq 18:78 )
313chain G and (resseq 18:78 )
413chain H and (resseq 18:78 )
513chain J and (resseq 18:78 )

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
ATPase GET3


Mass: 40464.730 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET3, ARR4, YDL100C, D2371 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12154, Hydrolases; Acting on acid anhydrides
#2: Protein
Golgi to ER traffic protein 1


Mass: 7896.763 Da / Num. of mol.: 5 / Fragment: Get1 cytosolic domain from residue 36 to 93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET1, MDM39, YGL020C / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53192
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 M LiCl, 20% PEG 6000, 0.1 M Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorDate: Nov 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3→51.3 Å / Num. obs: 56397 / % possible obs: 99.7 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 5.7 % / Rsym value: 0.123 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.16 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→51.3 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 2857 5.07 %random
Rwork0.1808 ---
obs0.1834 56397 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.981 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3516 Å2-0 Å20 Å2
2---0.8108 Å2-0 Å2
3---1.1624 Å2
Refinement stepCycle: LAST / Resolution: 3→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15830 0 38 5 15873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116119
X-RAY DIFFRACTIONf_angle_d1.15721699
X-RAY DIFFRACTIONf_dihedral_angle_d19.5016044
X-RAY DIFFRACTIONf_chiral_restr0.0732429
X-RAY DIFFRACTIONf_plane_restr0.0042813
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F2611X-RAY DIFFRACTIONPOSITIONAL
12I2611X-RAY DIFFRACTIONPOSITIONAL0.043
21B2603X-RAY DIFFRACTIONPOSITIONAL
22E2603X-RAY DIFFRACTIONPOSITIONAL0.05
31C515X-RAY DIFFRACTIONPOSITIONAL
32D515X-RAY DIFFRACTIONPOSITIONAL0.036
33G515X-RAY DIFFRACTIONPOSITIONAL0.037
34H515X-RAY DIFFRACTIONPOSITIONAL0.038
35J515X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.31972690.25295328X-RAY DIFFRACTION100
3.1072-3.23160.30262870.22345279X-RAY DIFFRACTION100
3.2316-3.37860.27012900.19415319X-RAY DIFFRACTION100
3.3786-3.55670.23143180.17225287X-RAY DIFFRACTION100
3.5567-3.77950.22922690.16155347X-RAY DIFFRACTION100
3.7795-4.07120.2112650.14915375X-RAY DIFFRACTION100
4.0712-4.48070.18483100.14415334X-RAY DIFFRACTION100
4.4807-5.12860.18222840.13455413X-RAY DIFFRACTION100
5.1286-6.45940.22832750.17225427X-RAY DIFFRACTION100
6.4594-51.27330.23252900.19875431X-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)
11.8009-0.84660.39932.49190.53952.2558-0.0633-0.0430.22750.07290.1048-0.0063-0.00820.2602-0.04880.0711-0.07-0.01050.0723-0.0230.088852.08358.3835-17.875
20.5090.70610.49360.2248-0.78870.2731-0.0336-0.0461-0.1789-0.0171-0.010.1022-0.18180.0588-0.04640.1760.06490.05150.1259-0.06410.511418.21568.5786-13.61
31.8447-0.28580.63032.43720.66931.0412-0.0903-0.0254-0.02810.06890.1192-0.11670.00970.16450.01090.16720.0909-0.01350.16850.0579-0.008853.8562-25.845-22.4941
40.8006-0.5080.08351.4081-1.1980.48830.04650.0598-0.3417-0.2384-0.03960.52040.06110.0464-0.00650.46090.0575-0.22650.1149-0.00940.345328.6711-26.6079-45.6289
52.0983-0.2392-0.33631.30280.23420.96260.10020.44030.19190.3456-0.36260.70020.2191-0.10540.30650.13330.01880.09970.1517-0.06190.476722.5314-11.9157-10.2541
60.2451-0.27750.08340.1043-0.24030.9270.32180.2166-0.4484-0.3113-0.17020.3771-0.21690.02970.02850.48190.1456-0.24390.2569-0.02930.440333.7285-6.0096-45.8986
71.8147-0.83590.16972.8386-0.37481.227-0.205-0.4486-0.06280.07410.31240.0867-0.2751-0.1065-0.04970.22730.07940.02720.31570.05840.111167.6417-0.5748-68.6044
80.6116-0.1337-0.21930.44971.61931.17460.0258-0.04560.0325-0.54720.057-0.1586-0.6185-0.0363-0.07530.8194-0.09680.08850.18170.03610.24273.6893-0.4774-102.0993
91.4995-0.6883-0.23142.298-0.06762.361-0.1365-0.1246-0.30460.0530.19390.0420.0166-0.0720.02420.0206-0.00080.04660.24050.2220.269671.6188-34.743-65.2833
101.40960.8775-0.51581.4098-0.30711.0415-0.0066-0.1314-0.0962-0.22140.1144-0.22010.170.0532-0.07430.2456-0.00540.15110.2688-0.02310.5585101.3838-35.7619-82.1121
110.5719-0.1583-0.10380.8403-0.36231.27840.3377-0.1935-0.2513-0.6252-0.1803-0.1562-0.61710.0638-0.25090.5959-0.01230.09130.16310.03760.175869.2972-21.0416-98.9774
121.6383-0.31080.37250.5778-0.60460.3417-0.1854-0.5581-0.3135-0.1941-0.2385-0.89710.16350.31020.26140.32510.00770.34160.35890.12770.7428100.0574-15.1181-77.2651
133.1218-0.3265-0.20384.12590.73442.13690.42550.6151-0.1181-1.2735-0.42910.0277-0.2739-0.0088-0.02890.4690.2788-0.13650.1815-0.153-0.070499.7635-17.1782-18.2385
140.4171-1.2405-0.20210.74270.16520.83490.2325-0.0244-0.25160.42920.02510.18120.42640.1127-0.16210.4709-0.04960.08670.15360.01290.290885.0732-17.610712.6075
151.0622-0.639-0.2780.76780.29971.15050.00870.0364-0.18470.3906-0.66830.42940.4001-0.20770.18320.7721-0.05330.16410.3288-0.05870.332783.24282.87267.5836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:354 ) )A5 - 88
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:354 ) )A158 - 170
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:354 ) )A233 - 354
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 89:157 OR RESID 172:232 ) )A89 - 157
5X-RAY DIFFRACTION2( CHAIN A AND ( RESID 89:157 OR RESID 172:232 ) )A172 - 232
6X-RAY DIFFRACTION3( CHAIN B AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:354 ) )B4 - 88
7X-RAY DIFFRACTION3( CHAIN B AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:354 ) )B158 - 170
8X-RAY DIFFRACTION3( CHAIN B AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:354 ) )B233 - 354
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 89:157 OR RESID 172:232 ) )B89 - 157
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 89:157 OR RESID 172:232 ) )B172 - 232
11X-RAY DIFFRACTION5( CHAIN C AND RESID 35:78 )C35 - 78
12X-RAY DIFFRACTION6( CHAIN D AND RESID 35:78 )D35 - 78
13X-RAY DIFFRACTION7( CHAIN E AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:353 ) )E5 - 88
14X-RAY DIFFRACTION7( CHAIN E AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:353 ) )E158 - 170
15X-RAY DIFFRACTION7( CHAIN E AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:353 ) )E233 - 353
16X-RAY DIFFRACTION8( CHAIN E AND ( RESID 89:157 OR RESID 172:232 ) )E89 - 157
17X-RAY DIFFRACTION8( CHAIN E AND ( RESID 89:157 OR RESID 172:232 ) )E172 - 232
18X-RAY DIFFRACTION9( CHAIN F AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:354 ) )F4 - 88
19X-RAY DIFFRACTION9( CHAIN F AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:354 ) )F158 - 170
20X-RAY DIFFRACTION9( CHAIN F AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:354 ) )F233 - 354
21X-RAY DIFFRACTION10( CHAIN F AND ( RESID 89:157 OR RESID 172:232 ) )F89 - 157
22X-RAY DIFFRACTION10( CHAIN F AND ( RESID 89:157 OR RESID 172:232 ) )F172 - 232
23X-RAY DIFFRACTION11( CHAIN G AND RESID 35:78 )G35 - 78
24X-RAY DIFFRACTION12( CHAIN H AND RESID 35:78 )H35 - 78
25X-RAY DIFFRACTION13( CHAIN I AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:353 ) )I5 - 88
26X-RAY DIFFRACTION13( CHAIN I AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:353 ) )I158 - 170
27X-RAY DIFFRACTION13( CHAIN I AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:353 ) )I233 - 353
28X-RAY DIFFRACTION14( CHAIN I AND ( RESID 89:157 OR RESID 172:232 ) )I89 - 157
29X-RAY DIFFRACTION14( CHAIN I AND ( RESID 89:157 OR RESID 172:232 ) )I172 - 232
30X-RAY DIFFRACTION15( CHAIN J AND RESID 35:78 )J35 - 78

+
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://pdbjlc1.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