[English] 日本語
Yorodumi
- PDB-2ck3: Azide inhibited bovine F1-ATPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ck3
TitleAzide inhibited bovine F1-ATPase
Components(ATP SYNTHASE SUBUNIT ...) x 5
KeywordsHYDROLASE
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / aerobic respiration / proton transmembrane transport / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, 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, 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, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Sandwich / 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 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AZIDE ION / PHOSPHATE ION / ATP synthase subunit beta, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBowler, M.W. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: How Azide Inhibits ATP Hydrolysis by the F-Atpases.
Authors: Bowler, M.W. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Reproducible Improvements in Order and Diffraction Limit of Crystals of Bovine Mitochondrial F(1)- ATPase by Controlled Dehydration.
Authors: Bowler, M.W. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
#2: Journal: Embo J. / Year: 2004
Title: The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride
Authors: Kagawa, R. / Montgomery, M.G. / Braig, K. / Leslie, A.G.W. / Walker, J.E.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Tructure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites Implications for the Mechanism of Rotary Catalysis
Authors: Menz, R.I. / Walker, J.E. / Leslie, A.G.W.
#4: Journal: Nat.Struct.Biol. / Year: 2000
Title: The Structure of the Central Stalk in Bovine F1- ATPase at 2.4A Resolution
Authors: Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
#5: Journal: Science / Year: 1999
Title: Molecular Architecture of the Rotary Motor in ATP Synthase
Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E.
#6: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1998
Title: ATP Synthesis by Rotary Catalysis (Nobel Lecture)
Authors: Walker, J.E.
#7: Journal: Nature / Year: 1994
Title: Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria
Authors: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E.
#8: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of F1-ATPase from Bovine Heart Mitochondria
Authors: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / Walker, J.E.
History
DepositionApr 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 22, 2014Group: Database references / Refinement description / Structure summary
Revision 1.3Dec 13, 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 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,81121
Polymers372,1009
Non-polymers2,71112
Water43,3802408
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41410 Å2
ΔGint-231.9 kcal/mol
Surface area108330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.160, 105.220, 122.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
ATP SYNTHASE SUBUNIT ... , 5 types, 9 molecules ABCDEFGHI

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


Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE
References: UniProt: P19483, H+-transporting two-sector ATPase
#2: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL / ATP SYNTHASE BETA CHAIN


Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE
References: UniProt: P00829, EC: 3.6.1.34, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / ATP SYNTHASE BETA CHAIN / F-ATPASE GAMMA SUBUNIT


Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / ATP SYNTHASE DELTA CHAIN / F-ATPASE DELTA SUBUNIT


Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE
References: UniProt: P05630, EC: 3.6.1.34, H+-transporting two-sector ATPase
#5: Protein/peptide ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / ATP SYNTHASE EPSILON CHAIN / ATPASE SUBUNIT EPSILON


Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE
References: UniProt: P05632, EC: 3.6.1.34, H+-transporting two-sector ATPase

-
Non-polymers , 6 types, 2420 molecules

#6: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2408 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsREFERENCE FOR THE ALPHA SUBUNIT J.E.WALKER, S.J.POWELL,O.VINAS, AND M.J.RUNSWICK, BIOCHEMISTRY,VOL ...REFERENCE FOR THE ALPHA SUBUNIT J.E.WALKER, S.J.POWELL,O.VINAS, AND M.J.RUNSWICK, BIOCHEMISTRY,VOL 28,PP 4702-4708, 1989. SER 481 GLY CHAINS A, B, AND C: THIS RESIDUE WAS IDENTIFIED AS A GLY FROM THE PROTEIN SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS RESIDUE WAS AGC (SER) IN THREE CLONES WHILE IN TWO OTHERS IT WAS GGC (GLY). THE DIFFERENCE WAS THOUGHT TO BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN THIS POSITION. CHAIN G, HEART ISOFORM WHICH LACKS C-TERMINAL ASP.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.2
Details: 50 MM TRIS-HCL PH 8.2, 200 MM NACL, 20 MM MGSO4, 250 UM AMP-PNP, 5 UM ADP, 3 MM NAN3, 0.004% (W/V) PHENYLMETHYLSULFONYL FLUORIDE AND 9% (W/V) POLYETHYLENE GLYCOL 6000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 18, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 244566 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0J
Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.961 / SU ML: 0.125 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 12048 5 %RANDOM
Rwork0.197 ---
obs-242123 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23874 0 164 2408 26446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02224464
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.98933115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14253136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91224.181012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.054154323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7515180
X-RAY DIFFRACTIONr_chiral_restr0.0770.23869
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218070
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.212581
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.217036
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.22443
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0150.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.2136
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2821.516074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.074225017
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.96139381
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9984.58085
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 847 -
Rwork0.262 16740 -
obs--98.88 %
Refinement TLS params.Method: refined / Origin x: 99.0354 Å / Origin y: 31.3778 Å / Origin z: 60.5258 Å
111213212223313233
T-0.1717 Å20.0065 Å20.0591 Å2--0.1495 Å2-0.0138 Å2---0.117 Å2
L0.5058 °2-0.1949 °2-0.345 °2-0.4232 °20.1914 °2--0.8551 °2
S0.0143 Å °-0.0546 Å °0.04 Å °0.0453 Å °0.0016 Å °0.1434 Å °0.0478 Å °-0.1141 Å °-0.0159 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2001 - 2008
2X-RAY DIFFRACTION1I2001 - 2007
3X-RAY DIFFRACTION1F2001 - 2484
4X-RAY DIFFRACTION1G2001 - 2113
5X-RAY DIFFRACTION1D2001 - 2383
6X-RAY DIFFRACTION1E2001 - 2247
7X-RAY DIFFRACTION1B2001 - 2409
8X-RAY DIFFRACTION1C2001 - 2379
9X-RAY DIFFRACTION1A2001 - 2380
10X-RAY DIFFRACTION1F600 - 601
11X-RAY DIFFRACTION1D600 - 1092
12X-RAY DIFFRACTION1E602
13X-RAY DIFFRACTION1B600 - 601
14X-RAY DIFFRACTION1C600 - 601
15X-RAY DIFFRACTION1A600 - 601
16X-RAY DIFFRACTION1H17 - 140
17X-RAY DIFFRACTION1I1 - 25
18X-RAY DIFFRACTION1F9 - 474
19X-RAY DIFFRACTION1G1 - 271
20X-RAY DIFFRACTION1D9 - 475
21X-RAY DIFFRACTION1E9 - 474
22X-RAY DIFFRACTION1B23 - 510
23X-RAY DIFFRACTION1C21 - 510
24X-RAY DIFFRACTION1A24 - 510

+
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