[English] 日本語
Yorodumi
- PDB-3oeh: Structure of four mutant forms of yeast F1 ATPase: beta-V279F -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oeh
TitleStructure of four mutant forms of yeast F1 ATPase: beta-V279F
Components(ATP synthase subunit ...) x 5
KeywordsHYDROLASE / ATP SYNTHASE / ATP PHOSPHATASE / F1F0 ATPASE / ATP SYNTHESIS / ADP / PO4 / MITOCHONDRIA
Function / homology
Function and homology information


: / Mitochondrial protein degradation / : / : / : / mitochondrial nucleoid / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...: / Mitochondrial protein degradation / : / : / : / mitochondrial nucleoid / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / 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 / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / 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 ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / 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 / 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 / ATP synthase, gamma subunit, helix hairpin domain / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsArsenieva, D. / Symersky, J. / Wang, Y. / Pagadala, V. / Mueller, D.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of mutant forms of the yeast f1 ATPase reveal two modes of uncoupling.
Authors: Arsenieva, D. / Symersky, J. / Wang, Y. / Pagadala, V. / Mueller, D.M.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_label_asym_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: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase subunit delta
I: ATP synthase subunit epsilon
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit alpha
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase subunit beta
P: ATP synthase subunit gamma
Q: ATP synthase subunit delta
R: ATP synthase subunit epsilon
S: ATP synthase subunit alpha
T: ATP synthase subunit alpha
U: ATP synthase subunit alpha
V: ATP synthase subunit beta
W: ATP synthase subunit beta
X: ATP synthase subunit beta
Y: ATP synthase subunit gamma
Z: ATP synthase subunit delta
1: ATP synthase subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,127,06957
Polymers1,119,11127
Non-polymers7,95830
Water00
1
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase subunit delta
I: ATP synthase subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,69019
Polymers373,0379
Non-polymers2,65310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit alpha
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase subunit beta
P: ATP synthase subunit gamma
Q: ATP synthase subunit delta
R: ATP synthase subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,69019
Polymers373,0379
Non-polymers2,65310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
S: ATP synthase subunit alpha
T: ATP synthase subunit alpha
U: ATP synthase subunit alpha
V: ATP synthase subunit beta
W: ATP synthase subunit beta
X: ATP synthase subunit beta
Y: ATP synthase subunit gamma
Z: ATP synthase subunit delta
1: ATP synthase subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,69019
Polymers373,0379
Non-polymers2,65310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.931, 291.896, 188.765
Angle α, β, γ (deg.)90.00, 101.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
ATP synthase subunit ... , 5 types, 27 molecules ABCJKLSTUDEFMNOVWXGPYHQZIR1

#1: Protein
ATP synthase subunit alpha


Mass: 55007.402 Da / Num. of mol.: 9 / Fragment: UNP RESIDUES 36-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATP1, YBL099W, YBL0827 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P07251, H+-transporting two-sector ATPase
#2: Protein
ATP synthase subunit beta


Mass: 52058.008 Da / Num. of mol.: 9 / Fragment: UNP RESIDUES 34-511 / Mutation: V279F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATP2, YJR121W, J2041 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P00830, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma / F-ATPase gamma subunit


Mass: 30657.160 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 34-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATP3, ATP3a, ATP3b, YBR039W, YBR0408 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P38077, H+-transporting two-sector ATPase
#4: Protein ATP synthase subunit delta / F-ATPase delta subunit


Mass: 14565.385 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 23-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATP16, YDL004W, YD8119.03, D2935 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q12165, H+-transporting two-sector ATPase
#5: Protein ATP synthase subunit epsilon / ATPase subunit epsilon


Mass: 6618.359 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 2-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATP15, YPL271W, P0345 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P21306, H+-transporting two-sector ATPase

-
Non-polymers , 2 types, 30 molecules

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


Mass: 506.196 Da / Num. of mol.: 15 / 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.: 15 / Source method: obtained synthetically / Formula: Mg

-
Details

Compound detailsCHAIN A, J, S: ALPHA SUBUNIT(E) CHAIN B, K, T: ALPHA SUBUNIT (TP) CHAIN C, L, U: ALPHA SUBUNIT (DP) ...CHAIN A, J, S: ALPHA SUBUNIT(E) CHAIN B, K, T: ALPHA SUBUNIT (TP) CHAIN C, L, U: ALPHA SUBUNIT (DP) CHAIN D, M, V: BETA SUBUNIT (DP) CHAIN E, N, W: BETA SUBUNIT (E) CHAIN F, O, X: BETA SUBUNIT (TP) CHAIN G, P, Y: GAMMA SUBUNIT CHAIN H, Q, Z: DELTA SUBUNIT CHAIN I, R, 1: EPSILON SUBUNIT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 277 K / pH: 7.3
Details: 5.5% PEG 6000, 10% GLYCEROL, 4% METHANOL, 0.05M SODIUM ACETATE, 0.5MM NICKEL SULPHATE, 0.5MM AMP/PNP, 0.025 MM ADP, 2MM MAGNESIUM CHLORIDE, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 203379 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 88.6 Å2 / Rsym value: 0.05 / Net I/σ(I): 14.1
Reflection shellResolution: 3→3.11 Å / Rsym value: 0.391 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HLD

2hld


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.892 / SU ML: 0.406 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: ENGH & HUBER
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4157 2 %RANDOM
Rwork0.209 ---
obs0.21 203286 88.81 %-
all-203286 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.4 Å2
Refine analyzeLuzzati coordinate error free: 0.508 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms72227 0 480 0 72707
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.16
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 289 -
Rwork0.284 13427 -
obs--81.04 %
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)
14.25550.40770.26648.5865-1.32021.5667-0.1454-0.9060.04760.93320.1675-0.2459-0.00930.2325-0.02210.4630.1507-0.10690.929-0.03580.399821.43461.163382.7173
22.96450.1687-0.51681.07140.50931.9176-0.1515-0.1908-0.19890.14120.06910.2540.0979-0.14240.08250.15480.11680.00580.48840.02130.6139-5.79953.639168.5685
36.31580.5478-1.01573.646-0.44755.1555-0.17010.65720.3236-0.49610.22190.5050.2741-0.7661-0.05180.16360.0358-0.11280.92440.08270.9885-31.02438.974751.8463
48.524-0.8807-4.27866.35851.63622.463-0.4507-0.5613-0.81070.05580.2703-0.8590.35510.22790.18040.48760.26530.03290.61710.18321.010335.4128-29.972458.8963
51.5725-0.1831-0.4114.53310.19012.0575-0.27310.189-0.517-1.43140.11320.00440.6299-0.15450.15991.0463-0.06780.0810.3311-0.09840.765121.2364-30.36331.3574
64.78921.18991.62940.8276-0.66914.71720.03380.5019-0.0459-0.46970.0399-0.0869-0.1228-0.2339-0.07372.1899-0.2516-0.22080.9019-0.2590.97563.5873-30.18116.4032
73.0823-0.6081-0.93686.32681.48895.2186-0.133-0.2162-0.0487-0.0433-0.0259-0.915-0.12210.78110.1590.0720.0405-0.00940.8226-0.05131.00852.44457.555455.1555
81.795-0.0887-0.36723.3226-0.25871.5802-0.03010.13520.26-0.72870.0787-0.4792-0.29030.1323-0.04860.4715-0.06430.13350.4061-0.08030.644334.97624.10336.0092
92.9982-0.66510.10776.0278-0.64534.2615-0.15840.44520.5092-1.2502-0.02480.5809-0.844-0.96060.18321.39930.0424-0.1120.87440.07680.685416.234736.885915.1294
1011.022-1.4852-5.10699.0254-2.90066.8388-0.2289-0.7532-0.01271.22180.1826-0.913-0.96731.1160.04640.329-0.0238-0.21030.8681-0.30830.632638.076417.432572.2283
112.37290.09440.29262.5847-0.40171.6681-0.08-0.28130.6009-0.03840.25730.115-0.5207-0.0595-0.17730.28610.0348-0.01610.5038-0.10850.665214.255129.522759.528
124.90571.922-0.34135.7479-1.67833.8621-0.31090.83920.716-1.5690.51490.9033-0.1839-0.6531-0.20410.73580.1039-0.35230.69480.26311.0299-8.606532.336738.7604
132.79314.00310.73277.65992.57643.60760.0409-0.6217-0.66860.82970.0861-0.4160.6464-0.0789-0.1270.4580.38160.03690.94250.42030.713218.5711-21.738776.0375
144.38950.1501-0.05251.95580.58941.8744-0.0524-0.077-0.527-0.1386-0.08850.66160.3735-0.45190.14090.4088-0.02030.01720.49960.05460.9114-2.8793-26.578155.9175
153.7460.6552-0.58243.06420.67645.81270.17841.2077-0.4046-0.948-0.2161.1598-0.1165-1.70940.03770.9073-0.019-0.40381.5374-0.2731.4885-24.2342-27.864934.166
166.21091.2425-0.7759.4071-0.20925.8259-0.3007-0.037-0.729-0.13690.1046-1.30720.5261.06330.19610.30380.27470.2110.6564-0.00271.116252.3608-17.144947.4628
172.0392-0.0262-0.26211.85420.01412.4698-0.10670.3212-0.2018-1.1871-0.0011-0.58310.40580.3350.10790.99680.03590.3440.4757-0.1190.719639.957-6.593522.7651
182.7859-0.00110.72172.67410.23493.52320.0230.8247-0.1014-1.5306-0.08470.4660.2068-0.70010.06181.603-0.0507-0.16150.9672-0.1010.588116.63523.55725.2444
193.1172-0.4407-1.5017.8881-0.41775.2517-0.027-0.3826-0.5358-0.21590.0191-0.9263-0.52121.78640.00790.3767-0.41590.08341.44060.08981.00633.9611-101.518171.5773
201.72290.0803-0.07312.8604-0.47893.87980.07030.3377-0.0419-0.9363-0.1371-0.3428-0.58380.71030.06680.8507-0.19490.2250.7973-0.03850.643118.1324-99.979144.897
211.89530.5496-0.08635.3234-0.30966.80140.10480.80390.2233-1.54030.12150.6645-0.3345-0.5764-0.22631.83810.0727-0.15821.0813-0.04760.8199-0.5157-100.23820.2999
220.8797-0.7955-0.63742.810.50983.88540.3076-0.16970.21590.1018-0.2788-0.3744-1.11990.3055-0.02881.7434-0.64230.05560.7206-0.22410.693413.5806-70.478490.2686
232.90010.0237-0.33782.4913-0.06670.51120.35910.12120.6943-0.0184-0.14780.5618-1.053-0.123-0.21132.2980.1930.18080.5236-0.12490.7709-15.1719-66.691677.5933
244.27971.1498-0.74720.48790.15942.66120.12880.32780.6656-0.3068-0.13110.6198-0.9696-0.9370.00232.43340.9183-0.15521.35380.03341.7293-41.5155-63.452563.042
255.483-1.38760.19094.2481-0.92595.96310.1192-0.9189-0.2680.3697-0.2123-0.4148-0.35350.48810.09320.4708-0.2701-0.07080.8840.03640.50497.333-109.0815103.2098
261.34371.0668-0.44752.3157-0.42263.1308-0.1245-0.0251-0.2004-0.2318-0.0643-0.03870.1254-0.270.18870.2237-0.09740.04390.5878-0.08960.5446-13.7247-122.266785.1022
273.7432-0.0421-1.03156.8522-0.90786.2385-0.10080.6312-0.3714-1.66150.24661.16330.8786-1.4192-0.14570.8521-0.4741-0.22351.176-0.18390.9254-35.4524-132.272666.0486
284.2162-2.0064-3.41714.46423.35666.2023-0.1226-0.7116-0.71760.1444-0.1091-0.97130.33781.30810.23170.3222-0.1145-0.01741.09940.24840.872122.934-118.530486.9319
292.00620.9467-0.1343.1576-0.91123.1273-0.0631-0.0095-0.44-0.4931-0.03440.14940.57540.50230.09750.48120.03050.15980.5613-0.00480.817.673-126.777662.7738
302.9570.19850.70592.3714-0.73165.31310.15790.5879-0.3466-0.86350.17181.17390.3132-1.0863-0.32981.0547-0.1509-0.2980.8501-0.03091.2783-15.6942-124.425242.4362
316.5922-3.6556-1.39515.8939-0.61081.33990.1887-0.26930.7060.5044-0.2337-1.1301-1.12920.96640.04511.5887-1.17980.02241.2584-0.05280.830129.2413-77.731671.6488
321.5481-0.6802-0.57262.1383-1.29614.42770.16330.46090.4427-0.3972-0.01770.0181-1.73260.0469-0.14552.1155-0.38270.10790.67830.06220.70818.598-69.735151.6309
336.35180.6645-1.82421.3262-0.38833.57860.26441.27390.3575-0.60720.09920.4039-0.9058-1.5293-0.36362.64760.4931-0.0071.8790.25731.1882-14.2574-65.206531.6225
348.25731.39240.17538.25980.20595.940.1752-1.29390.40790.8052-0.1069-0.3424-1.413-0.0995-0.06831.2641-0.4007-0.00640.8232-0.23540.41171.5237-84.1587106.0619
352.63210.09260.01332.031-0.27972.74540.2423-0.39540.26630.4619-0.20460.5542-1.0779-0.7094-0.03770.92260.10720.09940.7357-0.22140.6324-24.5623-91.562794.2676
364.2349-2.3190.37834.7483-1.1583.19730.3310.79060.1415-0.67330.01611.0734-0.6296-1.5116-0.34710.73130.3737-0.18261.5126-0.12791.0511-43.6992-98.017270.943
374.8896-1.80910.53717.8712-0.96193.0393-0.122-0.73190.06120.55680.0345-0.15251.1597-0.07370.08752.6126-0.49140.21781.2356-0.10840.645831.4559-34.8037184.1317
381.80310.2831-0.10825.0560.56352.70560.1489-0.13740.09950.975-0.13480.0750.3198-0.1119-0.01411.3736-0.1314-0.19450.5512-0.03930.667748.3954-20.8934162.813
393.87831.9932-0.52184.99330.91755.84480.21340.79040.0109-1.23770.2824-1.1556-0.34650.2307-0.49581.3871-0.05850.03670.8151-0.04161.21667.0462-11.0852140.8892
409.8767-2.8712-2.04061.9567-1.35075.26880.1502-0.54170.02260.482-0.08630.67250.1685-0.6876-0.0642.0252-0.92220.84681.8811-0.68261.5917-4.1013-34.712162.7456
412.6635-0.04971.19043.84680.35452.444-0.01450.27660.25360.0864-0.46271.06860.3637-1.13430.47721.16-0.41070.19351.6829-0.50151.20020.9494-33.1557132.3087
426.6114-0.88910.08274.5233-1.26770.49560.25621.34450.164-0.569-0.32980.07790.0861-0.4460.07351.8089-0.0723-0.24852.2492-0.35091.00918.2795-29.5184103.1722
433.8338-4.0135-0.01745.1485-1.27253.2553-0.2717-0.3352-0.80110.9321-0.08270.30150.0012-0.24910.35442.8673-0.82520.39191.30160.1151.269715.7238-70.8351169.4664
441.14610.57650.05791.47130.08010.8535-0.0387-0.2417-0.54940.70180.013-0.30440.6909-0.16110.02582.3944-0.3441-0.11570.97420.06681.041437.2718-73.3839147.711
454.97020.085-2.40541.53081.3322.4713-0.1203-0.00770.39380.07880.18810.04560.14480.4626-0.06782.5451-0.3414-0.30681.03060.23491.867556.27-73.0958123.755
468.82751.4595-2.94710.4211-0.94534.9980.2892-1.1124-0.65640.6714-0.101-0.0007-0.1449-0.5044-0.18823.1401-0.41620.10171.17720.15730.967733.7498-60.4271181.8965
471.80340.2736-0.60073.15580.14193.13570.0989-0.3387-0.52560.9419-0.0363-0.48790.96510.3876-0.06262.2315-0.0574-0.48010.64710.08331.021956.316-53.7963163.9571
482.5101-0.4267-1.3136.98130.68154.40520.16580.689-0.2263-0.76480.291-1.46070.58830.5585-0.45681.50630.1201-0.2391.0204-0.28731.546670.5779-45.5984137.6705
497.1965-1.53561.0824.1074-4.19414.8966-0.0489-0.92180.66290.64510.11670.56480.2881-0.5275-0.06782.2384-0.66420.64451.5275-0.54271.02814.196-21.1837174.3334
501.0260.4849-0.45553.03230.19644.31780.10540.03730.33730.3162-0.36940.17650.0446-0.76860.2641.0514-0.0315-0.011.0735-0.21830.895521.0613-9.2481147.8047
514.19652.2538-1.59414.4245-0.13166.709-0.23761.10340.5323-0.93320.1779-0.3113-0.4315-0.06640.05971.40420.2057-0.13881.40590.12940.998930.6693-0.8823120.1362
521.3893-2.2168-1.42933.91523.41135.8706-0.2371-0.0958-0.79940.73190.04041.04790.4928-0.92970.19672.2713-1.11410.74051.941-0.31411.5834-4.9934-58.7761159.3212
531.39180.9796-0.58882.69490.38741.2462-0.0397-0.0041-0.39380.4857-0.31880.86990.4602-0.81110.35841.8075-0.80760.2351.358-0.30541.19688.114-63.8107133.3062
544.58080.25641.97163.848-1.03394.3836-0.0580.18880.2477-0.2746-0.2724-0.32060.4388-0.24450.33041.4459-0.53140.12070.8033-0.33190.770328.4854-57.5694110.6566
5528.7266-3.211225.23362.3532-4.413323.86440.15260.11790.5989-0.99210.05720.3690.8329-0.3883-0.20980.98540.0385-0.19930.82650.0480.80563.71550.408434.6812
5610.15052.14493.46972.45460.84585.76920.3664-0.84210.10880.3974-0.2950.185-0.1995-0.3195-0.07140.9158-0.0162-0.03081.05720.04110.49-31.213117.21762.2296
5727.21762.888724.83390.91431.90123.9653-0.8413-0.21481.0658-0.41670.07110.4614-0.8176-0.7430.77021.12250.0621-0.21460.8941-0.13620.8779-15.1146-94.732656.8698
586.6232-0.90436.46433.48180.054613.7066-0.3121-0.5720.1765-0.13690.13110.2751-0.1987-1.40060.1810.8597-0.0491-0.20081.5494-0.10470.972-50.2466-103.66623.229
599.45625.4259-18.38513.7642-9.741839.4223-0.0664-0.7905-0.48840.2159-0.8274-0.52670.78611.41270.89381.5087-0.2925-0.00081.0953-0.03361.083937.1789-36.8724133.461
607.38951.6796-6.53482.7687-1.26428.60440.42650.7705-0.5827-0.2282-0.3679-0.6250.0546-0.0293-0.05861.6687-0.1857-0.08851.6168-0.20081.338560.3603-33.922697.0421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 97
2X-RAY DIFFRACTION2A98 - 382
3X-RAY DIFFRACTION3A383 - 509
4X-RAY DIFFRACTION4B25 - 97
5X-RAY DIFFRACTION5B98 - 382
6X-RAY DIFFRACTION6B383 - 509
7X-RAY DIFFRACTION7C26 - 97
8X-RAY DIFFRACTION8C98 - 382
9X-RAY DIFFRACTION9C383 - 509
10X-RAY DIFFRACTION10D6 - 82
11X-RAY DIFFRACTION11D83 - 357
12X-RAY DIFFRACTION12D358 - 475
13X-RAY DIFFRACTION13E8 - 82
14X-RAY DIFFRACTION14E83 - 357
15X-RAY DIFFRACTION15E358 - 475
16X-RAY DIFFRACTION16F7 - 82
17X-RAY DIFFRACTION17F83 - 357
18X-RAY DIFFRACTION18F358 - 475
19X-RAY DIFFRACTION19J26 - 97
20X-RAY DIFFRACTION20J98 - 382
21X-RAY DIFFRACTION21J383 - 509
22X-RAY DIFFRACTION22K21 - 97
23X-RAY DIFFRACTION23K98 - 382
24X-RAY DIFFRACTION24K383 - 509
25X-RAY DIFFRACTION25L26 - 97
26X-RAY DIFFRACTION26L98 - 382
27X-RAY DIFFRACTION27L383 - 509
28X-RAY DIFFRACTION28M6 - 82
29X-RAY DIFFRACTION29M83 - 357
30X-RAY DIFFRACTION30M358 - 475
31X-RAY DIFFRACTION31N6 - 82
32X-RAY DIFFRACTION32N83 - 357
33X-RAY DIFFRACTION33N358 - 475
34X-RAY DIFFRACTION34O7 - 82
35X-RAY DIFFRACTION35O83 - 357
36X-RAY DIFFRACTION36O358 - 474
37X-RAY DIFFRACTION37S27 - 97
38X-RAY DIFFRACTION38S98 - 382
39X-RAY DIFFRACTION39S383 - 509
40X-RAY DIFFRACTION40T26 - 97
41X-RAY DIFFRACTION41T98 - 382
42X-RAY DIFFRACTION42T383 - 509
43X-RAY DIFFRACTION43U26 - 97
44X-RAY DIFFRACTION44U98 - 382
45X-RAY DIFFRACTION45U383 - 509
46X-RAY DIFFRACTION46V6 - 82
47X-RAY DIFFRACTION47V83 - 357
48X-RAY DIFFRACTION48V358 - 475
49X-RAY DIFFRACTION49W8 - 82
50X-RAY DIFFRACTION50W83 - 357
51X-RAY DIFFRACTION51W358 - 474
52X-RAY DIFFRACTION52X7 - 82
53X-RAY DIFFRACTION53X83 - 357
54X-RAY DIFFRACTION54X358 - 475
55X-RAY DIFFRACTION55G1 - 25
56X-RAY DIFFRACTION55G234 - 276
57X-RAY DIFFRACTION56G26 - 233
58X-RAY DIFFRACTION56H11 - 136
59X-RAY DIFFRACTION56I8 - 61
60X-RAY DIFFRACTION57P1 - 25
61X-RAY DIFFRACTION57P234 - 276
62X-RAY DIFFRACTION58P26 - 233
63X-RAY DIFFRACTION58Q12 - 137
64X-RAY DIFFRACTION58R10 - 47
65X-RAY DIFFRACTION59Y1 - 25
66X-RAY DIFFRACTION59Y234 - 275
67X-RAY DIFFRACTION60Y26 - 233
68X-RAY DIFFRACTION60Z119 - 135
69X-RAY DIFFRACTION6019 - 45

+
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