[English] 日本語
Yorodumi
- PDB-5odi: Heterodisulfide reductase / [NiFe]-hydrogenase complex from Metha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5odi
TitleHeterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH
Components
  • (Heterodisulfide reductase, subunit ...) x 3
  • (Methyl-viologen reducing hydrogenase, subunit ...) x 3
KeywordsOXIDOREDUCTASE / Heterodisulfide reductase / [NiFe]-hydrogenase / FeS cluster / ferredoxin / CCG motif / methanogenesis / flavoprotein / flavin-based electron bifurcation / [2Fe-2S] cluster / macromolecular complex / anaerobic / thioredoxin / metabolism / oxydoreductase.
Function / homology
Function and homology information


dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / hydrogenase (acceptor) / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding ...dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / hydrogenase (acceptor) / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / 4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / 4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / 4Fe-4S dicluster domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / FAD-dependent oxidoreductase 2, FAD binding domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / FAD binding domain / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Pyridine nucleotide-disulphide oxidoreductase / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / ACETATE ION / 1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C ...Non-cubane [4Fe-4S]-cluster / ACETATE ION / 1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Heterodisulfide reductase, subunit C / Methyl-viologen reducing hydrogenase subunit D / Methyl-viologen reducing hydrogenase subunit G / Methyl-viologen reducing hydrogenase subunit A / Heterodisulfide reductase, subunit B / CoB--CoM heterodisulfide reductase iron-sulfur subunit A
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWagner, T. / Koch, J. / Ermler, U. / Shima, S.
CitationJournal: Science / Year: 2017
Title: Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Authors: Wagner, T. / Koch, J. / Ermler, U. / Shima, S.
History
DepositionJul 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heterodisulfide reductase, subunit A
B: Heterodisulfide reductase, subunit B
C: Heterodisulfide reductase, subunit C
D: Methyl-viologen reducing hydrogenase, subunit D
E: Methyl-viologen reducing hydrogenase, subunit G
F: Methyl-viologen reducing hydrogenase, subunit A
G: Heterodisulfide reductase, subunit A
H: Heterodisulfide reductase, subunit B
I: Heterodisulfide reductase, subunit C
J: Methyl-viologen reducing hydrogenase, subunit D
K: Methyl-viologen reducing hydrogenase, subunit G
L: Methyl-viologen reducing hydrogenase, subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,94558
Polymers451,69812
Non-polymers13,24746
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76530 Å2
ΔGint-886 kcal/mol
Surface area126510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)370.528, 97.077, 135.149
Angle α, β, γ (deg.)90.00, 109.43, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Heterodisulfide reductase, subunit ... , 3 types, 6 molecules AGBHCI

#1: Protein Heterodisulfide reductase, subunit A


Mass: 71591.672 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TCB9*PLUS
#2: Protein Heterodisulfide reductase, subunit B


Mass: 32075.318 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Details: This subunit contains two pentacoordinated non cubane [4Fe4S] clusters
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TCB4*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#3: Protein Heterodisulfide reductase, subunit C


Mass: 20483.650 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TC97*PLUS

-
Methyl-viologen reducing hydrogenase, subunit ... , 3 types, 6 molecules DJEKFL

#4: Protein Methyl-viologen reducing hydrogenase, subunit D


Mass: 16057.495 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TC98*PLUS
#5: Protein Methyl-viologen reducing hydrogenase, subunit G


Mass: 32511.432 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TC99*PLUS, hydrogen dehydrogenase
#6: Protein Methyl-viologen reducing hydrogenase, subunit A


Mass: 53129.602 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Details: The C-terminus has been post-translationally cleaved
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Variant: / / Tissue: /
References: UniProt: A0A2D0TCA6*PLUS, hydrogen dehydrogenase

-
Non-polymers , 12 types, 600 molecules

#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#9: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#14: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#15: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#16: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#17: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.28 %
Description: Black thick plate, square shape of about 0.2-0.4 mm length
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular ...Details: Crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK). The crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 1% (w/v) polyethylene glycol 3350, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD, 10 mM CoM-SH and 1 ul of precipitant. The crystals appear after 1-2 weeks and are cryoprotected in the crystallization solution supplemented with 30% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.4→48.54 Å / Num. obs: 176807 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 30.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.071 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 25737 / CC1/2: 0.332 / Rpim(I) all: 0.188 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ODC

5odc


Resolution: 2.4→48.54 Å / Cor.coef. Fo:Fc: 0.9146 / Cor.coef. Fo:Fc free: 0.8865 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.363 / SU Rfree Blow DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 8805 4.98 %RANDOM
Rwork0.2015 ---
obs0.2035 176789 99.94 %-
Displacement parametersBiso mean: 64.65 Å2
Baniso -1Baniso -2Baniso -3
1-4.2309 Å20 Å23.2754 Å2
2---1.1058 Å20 Å2
3----3.1251 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: 1 / Resolution: 2.4→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61987 0 1111 554 63652
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00663200HARMONIC8
X-RAY DIFFRACTIONt_angle_deg1.05114891HARMONIC8
X-RAY DIFFRACTIONt_dihedral_angle_d14257SINUSOIDAL6
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes820HARMONIC6
X-RAY DIFFRACTIONt_gen_planes9024HARMONIC40
X-RAY DIFFRACTIONt_it63200HARMONIC20
X-RAY DIFFRACTIONt_nbd39SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.29
X-RAY DIFFRACTIONt_other_torsion15.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4130SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact70328SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2942 682 5.23 %
Rwork0.2497 12357 -
all0.252 13039 -
obs--99.94 %
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)
10.43040.21110.46080.04080.25031.3599-0.18650.00390.2635-0.00610.03580.0602-0.0067-0.01020.15060.14190.0911-0.1614-0.15660.0320.058232.26578.431565.872
2-0.44182.39172.42532.32581.85641.766-0.00830.0004-0.0998-0.00740.0150.08460.072-0.0139-0.00670.12560.008-0.1593-0.0612-0.07930.036519.4158-39.364518.6808
3-0.317-0.31360.46131.93831.0212.12290.03110.0475-0.0834-0.0206-0.0276-0.01330.00340.0435-0.00350.12860.029-0.10170.0871-0.0424-0.102432.5597-24.397515.0932
4-0.0893-0.46011.45591.91131.09892.75310.00240.0452-0.03020.0192-0.0196-0.0294-0.00080.0380.01720.20870.1521-0.08-0.019-0.0016-0.071749.0119-1.8187.5342
50.63650.12990.88610-0.26472.20230.0046-0.03630.04760.0062-0.00930.07330.0135-0.02380.00470.19530.138-0.1134-0.0932-0.104-0.007654.45058.6261117.0241
60.62550.02790.77930.33940.09520.7858-0.0052-0.10940.09850.0733-0.0016-0.0661-0.05230.18570.00680.1280.0059-0.07330.1958-0.1547-0.163972.917914.6389133.0774
70.11070.05240.857900.51420.6658-0.1802-0.02810.06530.0224-0.1409-0.02070.2245-0.26780.32110.20.0534-0.05150.1138-0.0189-0.156510.273-3.249552.9836
80.89560.45790.10240.9118-0.46331.5476-0.0395-0.00240.1491-0.00580.0662-0.1087-0.01890.0337-0.02660.0210.0541-0.13850.2169-0.1015-0.119678.2183-4.317450.8114
91.6723-0.41910.28040.0201-0.39050.82420.0060.0179-0.02140.00240.02470.0134-0.01320.0627-0.03070.1450.1568-0.09430.1027-0.0804-0.105467.8326-21.532352.5198
101.6722-1.37010.586100.432.3842-0.0042-0.0021-0.01690.02220.0030.01640.00660.0360.00120.03560.158-0.15480.1383-0.0116-0.0647-0.87133.079226.3172
110.7833-0.31892.85170.31060.21312.95830.00090.02570.01360.11440.01150.00510.08070.0022-0.01250.04040.1706-0.16210.041-0.0339-0.0418-28.824513.738417.2336
120.52630.40732.10440.94180.68081.881-0.00290.1475-0.0590.1234-0.06440.15150.2127-0.12820.06730.0130.1451-0.17170.0848-0.11-0.0452-48.15039.58971.7863
130.1063-0.30330.79310.1557-0.04991.2567-0.0152-0.00250.00590.0187-0.00760.00340.0292-0.02650.02280.03720.0302-0.03470.00490.0059-0.018823.35690.534757.5937
140.4790.61210.52440.09070.35930.6012-0.0125-0.01740.0836-0.2714-0.04780.0860.0091-0.07960.06020.09260.1580.121-0.04730.0089-0.111920.47143.533960.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ S|* }
14X-RAY DIFFRACTION14{ W|* }

+
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