[English] 日本語
Yorodumi
- PDB-2wpd: The Mg.ADP inhibited state of the yeast F1c10 ATP synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wpd
TitleThe Mg.ADP inhibited state of the yeast F1c10 ATP synthase
Components(ATP SYNTHASE SUBUNIT ...) x 6
KeywordsHYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP-BINDING / CENTRAL STALK / ATP SYNTHESIS / PHOSPHOPROTEIN / MEMBRANE PROTEIN / LIPID-BINDING / ION TRANSPORT / NUCLEOTIDE-BINDING / HYDROGEN ION TRANSPORT
Function / homology
Function and homology information


Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism ...Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / F1F0 ATP synthase subunit C / F1FO ATP Synthase ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.432 Å
AuthorsDautant, A. / Velours, J. / Giraud, M.-F.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Crystal Structure of the Mg.Adp-Inhibited State of the Yeast F1C10-ATP Synthase.
Authors: Dautant, A. / Velours, J. / Giraud, M.
#1: Journal: Science / Year: 1999
Title: Molecular Architecture of the Rotary Motor in ATP Synthase.
Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E.
#2: Journal: Embo J. / Year: 2006
Title: Novel Features of the Rotary Catalytic Mechanism Revealed in the Structure of Yeast F1 ATPase.
Authors: Kabaleeswaran, V. / Puri, N. / Walker, J.E. / Leslie, A.G.W. / Mueller, D.M.
#3: Journal: J.Biol.Chem. / Year: 2009
Title: Asymmetric Structure of the Yeast F1 ATPase in the Absence of Bound Nucleotides.
Authors: Kabaleeswaran, V. / Shen, H. / Symersky, J. / Walker, J.E. / Leslie, A.G.W. / Mueller, D.M.
#4: Journal: Science / Year: 2005
Title: Structure of the Rotor Ring of F-Type Na+-ATPase from Ilyobacter Tartaricus.
Authors: Meier, T. / Polzer, P. / Diederichs, K. / Welte, W. / Dimroth, P.
#5: Journal: J.Bioenerg.Biomembr. / Year: 2009
Title: Hydrogenated and Fluorinated Surfactants Derived from Tris(Hydroxymethyl)-Acrylamidomethane Allow the Purification of a Highly Active Yeast F1-F0 ATP-Synthase with an Enhanced Stability.
Authors: Talbot, J.-C. / Dautant, A. / Polidori, A. / Pucci, B. / Cohen-Bouhacina, T. / Maali, A. / Salin, B. / Brethes, D. / Velours, J. / Giraud, M.-F.
History
DepositionAug 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
D: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
E: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
F: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
G: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
H: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
J: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,52829
Polymers448,03019
Non-polymers2,49710
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32020 Å2
ΔGint-390 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.990, 173.944, 137.016
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN J AND (RESID 1:34 OR RESID 44:76)
211CHAIN K AND (RESID 1:34 OR RESID 44:76)
311CHAIN L AND (RESID 1:34 OR RESID 44:76)
411CHAIN M AND (RESID 1:34 OR RESID 44:76)
511CHAIN N AND (RESID 1:34 OR RESID 44:76)
611CHAIN O AND (RESID 1:34 OR RESID 44:76)
711CHAIN P AND (RESID 1:34 OR RESID 44:76)
811CHAIN Q AND (RESID 1:34 OR RESID 44:76)
911CHAIN R AND (RESID 1:34 OR RESID 44:76)
1011CHAIN S AND (RESID 1:34 OR RESID 44:76)

-
Components

-
ATP SYNTHASE SUBUNIT ... , 6 types, 19 molecules ABCDEFGHIJKLMNOPQRS

#1: Protein ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL / ATP SYNTHASE ALPHA CHAIN\ / MITOCHONDRIAL


Mass: 55007.402 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: P07251
#2: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL / ATP SYNTHASE BETA CHAIN\ / MITOCHONDRIAL


Mass: 51181.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A
References: UniProt: P00830, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / ATP SYNTHASE GAMMA CHAIN\ / MITOCHONDRIAL / F-ATPASE GAMMA SUBUNIT


Mass: 30657.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: P38077
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / ATP SYNTHASE DELTA CHAIN\ / MITOCHONDRIAL / F-ATPASE DELTA SUBUNIT


Mass: 14565.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: Q12165
#5: Protein ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / ATP SYNTHASE EPSILON CHAIN\ / MITOCHONDRIAL


Mass: 6618.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-62 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A / References: UniProt: P21306
#6: Protein
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL / ATP SYNTHASE 9 CHAIN\ / MITOCHONDRIAL / LIPID-BINDING PROTEIN / OLIGOMYCIN RESISTANCE PROTEIN 1


Mass: 7762.375 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: D273-10B/A
References: UniProt: P61829, H+-transporting two-sector ATPase

-
Non-polymers , 3 types, 10 molecules

#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.67 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES/HCL PH 7.5, 12% PEG MME 5000, 100 MM SODIUM CHLORIDE MIXED 1:1 WITH PROTEIN SOLUTION CONTAINING 0.64 MM DDM, 25 MM TRIS/HCL PH 8.0, 100 MM SODIUM CHLORIDE, 25 MM TREHALOSE, 0.5 ...Details: 0.1 M HEPES/HCL PH 7.5, 12% PEG MME 5000, 100 MM SODIUM CHLORIDE MIXED 1:1 WITH PROTEIN SOLUTION CONTAINING 0.64 MM DDM, 25 MM TRIS/HCL PH 8.0, 100 MM SODIUM CHLORIDE, 25 MM TREHALOSE, 0.5 MM EDTA, 0.02% SODIUM AZIDE, 2 MM MAGNESIUM CHLORIDE, 0.66 MM ADP, 0.1 MM DCCD, 2.5 MM DTT, 0.5 MM PMSF

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.43→39.8 Å / Num. obs: 84424 / % possible obs: 88.1 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 85 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.3
Reflection shellResolution: 3.43→3.62 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.3 / % possible all: 64.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HLD, 1YCE

2hld

1yce


Resolution: 3.432→39.775 Å / SU ML: 0.67 / σ(F): 1.34 / Phase error: 32.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 3767 5.1 %
Rwork0.2863 --
obs0.2868 74395 88.13 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.559 Å2 / ksol: 0.281 e/Å3
Displacement parametersBiso mean: 108 Å2
Baniso -1Baniso -2Baniso -3
1-7.3833 Å20 Å228.4471 Å2
2---13.2772 Å20 Å2
3---5.8939 Å2
Refinement stepCycle: LAST / Resolution: 3.432→39.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30674 0 152 0 30826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431294
X-RAY DIFFRACTIONf_angle_d0.62942421
X-RAY DIFFRACTIONf_dihedral_angle_d16.7111370
X-RAY DIFFRACTIONf_chiral_restr0.0325046
X-RAY DIFFRACTIONf_plane_restr0.0035446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11J480X-RAY DIFFRACTIONPOSITIONAL
12K480X-RAY DIFFRACTIONPOSITIONAL0
13L480X-RAY DIFFRACTIONPOSITIONAL0
14M480X-RAY DIFFRACTIONPOSITIONAL0
15N480X-RAY DIFFRACTIONPOSITIONAL0
16O480X-RAY DIFFRACTIONPOSITIONAL0
17P480X-RAY DIFFRACTIONPOSITIONAL0
18Q480X-RAY DIFFRACTIONPOSITIONAL0
19R480X-RAY DIFFRACTIONPOSITIONAL0
110S480X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4323-3.47570.4065900.39681770X-RAY DIFFRACTION60
3.4757-3.52140.37311040.39962004X-RAY DIFFRACTION68
3.5214-3.56960.39731130.39532063X-RAY DIFFRACTION69
3.5696-3.62060.361180.37292044X-RAY DIFFRACTION70
3.6206-3.67460.34891070.36042100X-RAY DIFFRACTION71
3.6746-3.7320.38561240.3752622X-RAY DIFFRACTION88
3.732-3.79310.37131230.37572688X-RAY DIFFRACTION90
3.7931-3.85840.34221520.35442708X-RAY DIFFRACTION91
3.8584-3.92850.35341410.34822690X-RAY DIFFRACTION92
3.9285-4.0040.37941550.34332739X-RAY DIFFRACTION93
4.004-4.08570.31741330.33492772X-RAY DIFFRACTION93
4.0857-4.17440.3541460.32082771X-RAY DIFFRACTION93
4.1744-4.27140.31371420.31652782X-RAY DIFFRACTION94
4.2714-4.37810.34771490.30172765X-RAY DIFFRACTION94
4.3781-4.49630.30851470.2952797X-RAY DIFFRACTION94
4.4963-4.62850.31591370.26982786X-RAY DIFFRACTION94
4.6285-4.77760.28651470.26632811X-RAY DIFFRACTION94
4.7776-4.94810.27811610.26272792X-RAY DIFFRACTION94
4.9481-5.14580.24341520.25952804X-RAY DIFFRACTION95
5.1458-5.37940.28311630.26162782X-RAY DIFFRACTION94
5.3794-5.66230.2671470.2642810X-RAY DIFFRACTION94
5.6623-6.01590.29271580.26112763X-RAY DIFFRACTION94
6.0159-6.47860.30341570.25962797X-RAY DIFFRACTION93
6.4786-7.12720.25331590.24022747X-RAY DIFFRACTION93
7.1272-8.15080.24531530.20572762X-RAY DIFFRACTION93
8.1508-10.24010.17511500.1722759X-RAY DIFFRACTION92
10.2401-39.77730.23971390.25472700X-RAY DIFFRACTION88

+
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