[English] 日本語
Yorodumi
- PDB-2h88: Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h88
TitleAvian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution
Components(SUCCINATE DEHYDROGENASE ...) x 4
KeywordsOXIDOREDUCTASE / COMPLEX II / MEMBRANE PROTEIN / HEME PROTEIN / IRON SULFUR PROTEIN / CYTOCHROME B / REDOX ENZYME / RESPIRATORY CHAIN / OXALOACETATE / UBIQUINONE
Function / homology
Function and homology information


The tricarboxylic acid cycle / succinate metabolic process / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration ...The tricarboxylic acid cycle / succinate metabolic process / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / 3 iron, 4 sulfur cluster binding / protein transmembrane transporter activity / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Single helix bin / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit ...Single helix bin / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Rhinovirus 14, subunit 4 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / hexyl beta-D-galactopyranoside / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / IRON/SULFUR CLUSTER / MALATE LIKE INTERMEDIATE / Unknown ligand ...AZIDE ION / hexyl beta-D-galactopyranoside / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / IRON/SULFUR CLUSTER / MALATE LIKE INTERMEDIATE / Unknown ligand / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 1.74 Å
AuthorsHuang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A.
Citation
Journal: Biochim.Biophys.Acta
Title: Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the
Authors: Huang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
Authors: Huang, L.S. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A
Authors: Huang, L.S. / Borders, T.M. / Shen, J.T. / Wang, C.J. / Berry, E.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2005
Title: Crystal structure of mitochondrial respiratory membrane protein complex II.
Authors: Sun, F. / Huo, X. / Zhai, Y. / Wang, A. / Xu, J. / Su, D. / Bartlam, M. / Rao, Z.
History
DepositionJun 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jul 29, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DO NOT MATCH TO ANY OF THE DATABASE ...SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DO NOT MATCH TO ANY OF THE DATABASE SEQUENCE. THE SEQUENCE OF SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT IS NOT AVAILABLE IN ANY OF THE DATABASE SEQUENCE AT THE TIME OF PROCESSING.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: Succinate dehydrogenase Ip subunit
C: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
D: Succinate dehydrogenase cytochrome B, small subunit
N: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
O: Succinate dehydrogenase Ip subunit
P: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
Q: Succinate dehydrogenase cytochrome B, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,28094
Polymers246,6128
Non-polymers5,66886
Water36,5702030
1
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: Succinate dehydrogenase Ip subunit
C: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
D: Succinate dehydrogenase cytochrome B, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,14045
Polymers123,3064
Non-polymers2,83441
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22640 Å2
ΔGint-127 kcal/mol
Surface area39970 Å2
MethodPISA, PQS
2
N: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
O: Succinate dehydrogenase Ip subunit
P: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
Q: Succinate dehydrogenase cytochrome B, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,14049
Polymers123,3064
Non-polymers2,83445
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22650 Å2
ΔGint-129 kcal/mol
Surface area40300 Å2
MethodPISA, PQS
3
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
hetero molecules

B: Succinate dehydrogenase Ip subunit
C: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
D: Succinate dehydrogenase cytochrome B, small subunit
O: Succinate dehydrogenase Ip subunit
P: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
Q: Succinate dehydrogenase cytochrome B, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,02479
Polymers178,3557
Non-polymers4,66972
Water1267
TypeNameSymmetry operationNumber
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area37180 Å2
ΔGint-247 kcal/mol
Surface area88390 Å2
MethodPISA
4
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
hetero molecules

O: Succinate dehydrogenase Ip subunit
P: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
Q: Succinate dehydrogenase cytochrome B, small subunit
hetero molecules

B: Succinate dehydrogenase Ip subunit
C: SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
D: Succinate dehydrogenase cytochrome B, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,02479
Polymers178,3557
Non-polymers4,66972
Water1267
TypeNameSymmetry operationNumber
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Buried area35430 Å2
ΔGint-248 kcal/mol
Surface area90140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.972, 199.391, 68.063
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
SUCCINATE DEHYDROGENASE ... , 4 types, 8 molecules ANBOCPDQ

#1: Protein SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT


Mass: 68256.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q9YHT1, succinate dehydrogenase
#2: Protein Succinate dehydrogenase Ip subunit


Mass: 28685.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q9YHT2, succinate dehydrogenase
#3: Protein SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT


Mass: 15392.052 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VWW3*PLUS, succinate dehydrogenase
#4: Protein Succinate dehydrogenase cytochrome B, small subunit


Mass: 10971.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZIS0, succinate dehydrogenase

-
Sugars , 1 types, 2 molecules

#14: Sugar ChemComp-BHG / hexyl beta-D-galactopyranoside / 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / hexyl beta-D-galactoside / hexyl D-galactoside / hexyl galactoside


Type: D-saccharide / Mass: 264.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H24O6

-
Non-polymers , 11 types, 2114 molecules

#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-TEO / MALATE LIKE INTERMEDIATE


Mass: 132.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O5
#9: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 64 / Source method: obtained synthetically
#10: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#12: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#13: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#15: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2030 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0025 M FUMARATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA. Type 1 ...Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0025 M FUMARATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA. Type 1 orthorhombic crystalls grew initially, after 1 month these monoclinic crystals appeared., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2005
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→60 Å / Num. all: 292236 / Num. obs: 292236 / % possible obs: 91.3 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.122 / Net I/σ(I): 12.8
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.89 / Num. unique all: 8881 / Rsym value: 0.99 / % possible all: 55.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
BOSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: 2FBW
Resolution: 1.74→45.14 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 14469 5 %RANDOM
Rwork0.178 ---
all0.1794 291095 --
obs0.1794 291095 89.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.5341 Å2 / ksol: 0.360845 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å20 Å21.16 Å2
2--5.1 Å20 Å2
3----1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.74→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16970 0 414 2030 19414
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.011.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it3.232
X-RAY DIFFRACTIONc_scangle_it4.62.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.74-1.780.3844445.10.33882410.018868540.2
1.79-1.820.33224100.3206801065
1.98-2.020.25246520.21611192196

+
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://pdbjlvh1.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