[English] 日本語
Yorodumi
- PDB-2jj2: The Structure of F1-ATPase inhibited by quercetin. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jj2
TitleThe Structure of F1-ATPase inhibited by quercetin.
Components
  • (ATP SYNTHASE SUBUNIT ...) x 2
  • ATP SYNTHASE GAMMA CHAIN
KeywordsHYDROLASE / ATP PHOSPHORYLASE / ATP SYNTHESIS
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven 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 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, gamma subunit conserved site ...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 / ATP synthase, gamma subunit, helix hairpin 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 / 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. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / ATP synthase subunit beta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Mechanism of Inhibition of Bovine F1-ATPase by Resveratrol and Related Polyphenols.
Authors: Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
History
DepositionJul 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 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 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-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 "HA" 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 "IA" 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 "JA" 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 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 HEART ISOFORM
B: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
C: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE GAMMA CHAIN
H: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
I: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
J: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
K: ATP SYNTHASE SUBUNIT BETA
L: ATP SYNTHASE SUBUNIT BETA
M: ATP SYNTHASE SUBUNIT BETA
N: ATP SYNTHASE GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)710,04252
Polymers702,91214
Non-polymers7,13138
Water40,2462234
1
A: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
B: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
C: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,02126
Polymers351,4567
Non-polymers3,56519
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41380 Å2
ΔGint-219.1 kcal/mol
Surface area101570 Å2
MethodPISA
2
H: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
I: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
J: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
K: ATP SYNTHASE SUBUNIT BETA
L: ATP SYNTHASE SUBUNIT BETA
M: ATP SYNTHASE SUBUNIT BETA
N: ATP SYNTHASE GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,02126
Polymers351,4567
Non-polymers3,56519
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41410 Å2
ΔGint-219.8 kcal/mol
Surface area101520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.399, 282.019, 138.093
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12B
22I
13C
23J
14D
24K
15E
25L
16F
26M
17G
27N

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A24 - 510
2112H24 - 510
1122B23 - 401
2122I23 - 401
1222B410 - 510
2222I410 - 510
1132C13 - 510
2132J13 - 510
1142D9 - 475
2142K9 - 475
1152E9 - 474
2152L9 - 474
1162F9 - 474
2162M9 - 474
1172G1 - 47
2172N1 - 47
1272G67 - 90
2272N67 - 90
1372G105 - 116
2372N105 - 116
1472G127 - 148
2472N127 - 148
1572G159 - 173
2572N159 - 173
1672G201 - 272
2672N201 - 272

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper: (Code: given
Matrix: (0.99999, 0.00102, 0.00336), (0.00102, -1, -0.00246), (0.00336, 0.00246, -0.99999)
Vector: -53.32538, 0.12465, 69.1796)

-
Components

-
ATP SYNTHASE SUBUNIT ... , 2 types, 12 molecules ABCHIJDEFKLM

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


Mass: 55332.219 Da / Num. of mol.: 6 / Fragment: RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein
ATP SYNTHASE SUBUNIT BETA / / ATP SYNTHASE BETA CHAIN


Mass: 51757.836 Da / Num. of mol.: 6 / Fragment: RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / References: UniProt: P00829, EC: 3.6.1.34

-
Protein , 1 types, 2 molecules GN

#3: Protein ATP SYNTHASE GAMMA CHAIN


Mass: 30185.674 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-297 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / References: UniProt: P05631, EC: 3.6.1.34

-
Non-polymers , 8 types, 2272 molecules

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


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#9: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#10: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN / Quercetin


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2234 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsRESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDONE CARBOXYLIC ACID RESIDUE ...RESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDONE CARBOXYLIC ACID RESIDUE AFTER TRANSIT TO MITOCHONDRION. THIS RESIDUE IS MODELLED HERE AS GLU.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.13 % / Description: NONE
Crystal growpH: 8.2 / Details: pH 8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→80.58 Å / Num. obs: 297401 / % possible obs: 94.3 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 88.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0J

1w0j


Resolution: 2.4→80.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 16.356 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 15035 5.1 %RANDOM
Rwork0.188 ---
obs0.19 282316 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20.63 Å2
2---0.33 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.4→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46072 0 444 2234 48750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02247280
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.99463922
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34956028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20824.1871944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.679158340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.16615346
X-RAY DIFFRACTIONr_chiral_restr0.0740.27416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0234878
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.223735
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.232831
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.23200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.166330722
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.037548140
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.26718420
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8381015772
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1948tight positional0.050.1
12H1948tight positional0.050.1
21B1916tight positional0.040.1
22I1916tight positional0.040.1
31C1980tight positional0.050.1
32J1980tight positional0.050.1
41D1868tight positional0.040.1
42K1868tight positional0.040.1
51E1864tight positional0.040.1
52L1864tight positional0.040.1
61F1864tight positional0.040.1
62M1864tight positional0.040.1
71G668tight positional0.030.1
72N668tight positional0.030.1
11A1767medium positional0.140.3
12H1767medium positional0.140.3
21B1742medium positional0.120.3
22I1742medium positional0.120.3
31C1788medium positional0.150.3
32J1788medium positional0.150.3
41D1671medium positional0.150.3
42K1671medium positional0.150.3
51E1666medium positional0.150.3
52L1666medium positional0.150.3
61F1666medium positional0.170.3
62M1666medium positional0.170.3
71G628medium positional0.140.3
72N628medium positional0.140.3
11A1948tight thermal0.975
12H1948tight thermal0.975
21B1916tight thermal0.885
22I1916tight thermal0.885
31C1980tight thermal0.975
32J1980tight thermal0.975
41D1868tight thermal0.915
42K1868tight thermal0.915
51E1864tight thermal0.795
52L1864tight thermal0.795
61F1864tight thermal0.95
62M1864tight thermal0.95
71G668tight thermal0.675
72N668tight thermal0.675
11A1767medium thermal1.8110
12H1767medium thermal1.8110
21B1742medium thermal1.6310
22I1742medium thermal1.6310
31C1788medium thermal1.8910
32J1788medium thermal1.8910
41D1671medium thermal1.7410
42K1671medium thermal1.7410
51E1666medium thermal1.4810
52L1666medium thermal1.4810
61F1666medium thermal1.7810
62M1666medium thermal1.7810
71G628medium thermal1.410
72N628medium thermal1.410
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 963
Rwork0.276 18771
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)
12.8727-0.35940.00740.4273-0.00851.69330.11720.2389-0.17-0.1599-0.00750.010.3562-0.0296-0.10970.10490.1128-0.0184-0.1496-0.0587-0.206-13.04131.8086-22.8493
20.58090.0748-0.03860.373-0.26650.5538-0.01410.19860.0543-0.0536-0.0739-0.00370.09190.12450.0881-0.10930.07320.00850.01450.1085-0.192-5.509231.6356-27.8341
30.1938-0.031-0.26762.0156-0.9242.87410.22350.06820.08460.1363-0.277-0.1754-0.3364-0.00780.0535-0.08780.05080.0173-0.09740.2466-0.072-1.141862.3576-28.6507
42.2753-0.4463-0.04081.20030.49363.66090.02810.186-0.2004-0.0469-0.085-0.00720.29440.25730.05690.00330.2211-0.0054-0.18780.0765-0.04412.2715-3.73879.6561
50.5199-0.10080.3270.1831-0.0850.9681-0.02450.07460.05210.0493-0.09320.00260.0370.22930.1177-0.15780.0378-0.0539-0.04710.1459-0.079319.791722.9722.7701
62.93790.83010.52862.23950.71752.02680.1603-0.24610.49210.2733-0.0893-0.0889-0.50450.3832-0.071-0.0525-0.1898-0.1417-0.13210.06240.021828.820750.066733.8633
71.60690.6525-0.99412.7823-0.53980.70840.074-0.1404-0.09350.0387-0.14810.07230.2656-0.02380.07410.0254-0.1028-0.0217-0.17190.0904-0.1171-29.1056-3.876516.1611
80.2877-0.08510.14760.5069-0.09270.59680.0237-0.07250.02480.0462-0.0094-0.00680.0388-0.1437-0.0143-0.15370.0130.0283-0.05350.0218-0.1267-35.935327.642618.4914
91.3345-0.3852-0.68132.0261.14260.8152-0.0919-0.16560.237-0.0202-0.0248-0.0742-0.3002-0.1960.1167-0.10540.1846-0.019-0.1262-0.1008-0.0426-40.311957.944520.2335
101.0853-0.1072-0.15441.0617-0.21572.6170.04220.0571-0.0888-0.0102-0.0435-0.00240.3094-0.20050.0013-0.0067-0.0706-0.0501-0.1718-0.0066-0.1207-33.45341.8894-7.0712
110.5950.0665-0.27960.3396-0.04180.53840.02880.07110.1424-0.0835-0.01310.02070.0548-0.12-0.0158-0.13980.047-0.043-0.06230.0574-0.1222-35.232630.6095-12.8451
121.1314-0.5392-0.64252.15340.37162.10270.226-0.01690.677-0.04350.0679-0.0375-0.61720.0148-0.2939-0.00910.09810.0604-0.29490.02890.1256-28.479560.2278-6.96
132.5595-0.06030.72080.422-0.35210.47010.05210.3741-0.2213-0.1331-0.1307-0.20130.31290.16850.07860.00820.26590.0661-0.0304-0.0065-0.15089.64351.4545-15.6614
140.6622-0.00370.15390.525-0.08370.81290.03420.21040.0425-0.0024-0.2071-0.08690.06480.30220.1729-0.23840.09920.03050.1260.2287-0.124322.853627.6369-10.8647
152.5836-0.5127-0.75574.44310.03381.82670.08590.19820.66640.2379-0.3213-0.1505-0.77360.64790.2354-0.2316-0.2668-0.0424-0.03610.39180.155231.477256.8522-6.5616
163.2923-0.8942-0.30711.17860.25112.95150.1056-0.1388-0.22710.0351-0.0896-0.06980.48670.0814-0.0160.07090.013-0.0526-0.2520.1568-0.0778-4.8207-4.43426.0427
170.5809-0.01210.38010.3777-0.18950.33610.0143-0.13880.01990.0656-0.0575-0.03860.0041-0.03530.0432-0.05620.0039-0.0157-0.07450.0656-0.1454-8.528322.722436.9025
180.8120.2255-0.5011.66220.44970.5259-0.1246-0.16620.3240.14160.0901-0.1903-0.3343-0.05120.03460.01880.0287-0.0863-0.2137-0.0752-0.0375-7.470653.443834.7267
190.97034.62260.586422.74862.97461.08210.02360.01980.0485-0.6669-0.14740.1377-0.28970.00350.1238-0.05310.0427-0.0412-0.15280.078-0.1203-1.779548.49414.7383
206.11190.6162-1.059421.52144.8495.66220.3044-0.21190.7323-0.153-0.12980.0229-0.82720.3082-0.17460.1553-0.12770.1299-0.693-0.00250.02960.523183.260812.4661
213.3053-0.34110.42911.82250.18552.7077-0.0334-0.22230.08190.20510.0554-0.0478-0.34910.0166-0.0220.0844-0.08810.0112-0.1603-0.0544-0.21440.0672-1.857492.1589
220.628-0.21290.08910.5186-0.34290.713-0.002-0.2066-0.0690.045-0.0913-0.0121-0.12170.12630.0933-0.1001-0.091-0.02220.01760.1176-0.20447.5447-31.688897.1116
230.30220.2852-0.37912.4572-0.54582.29680.1981-0.1217-0.2364-0.0816-0.2602-0.15210.20990.0690.0621-0.0881-0.0576-0.0254-0.09120.2461-0.071351.7973-62.430497.8958
242.64030.1439-0.06980.8924-0.19874.11840.103-0.14230.1590.1206-0.0633-0.1314-0.37940.1481-0.03970.0322-0.2291-0.0026-0.19930.0834-0.073565.45013.769459.7556
250.59530.0085-0.39820.3585-0.08370.9684-0.0061-0.1128-0.0764-0.0622-0.1216-0.0301-0.00730.22910.1277-0.1658-0.05320.0408-0.0450.1626-0.080772.9893-22.889746.6008
262.2302-0.86670.34463.00790.01423.50420.20620.3322-0.4713-0.3529-0.03190.03450.52410.5593-0.1744-0.02760.23860.1611-0.14640.06630.018282.0344-49.967635.4329
271.87160.08360.31642.2815-0.06770.51520.08290.15510.0293-0.0043-0.07970.0063-0.2828-0.0915-0.00320.02360.1030.0365-0.16390.1101-0.141624.04813.900853.1485
280.3680.1055-0.28160.3409-0.04960.78190.00120.10990.0009-0.00770.01540.003-0.0143-0.1272-0.0166-0.1618-0.0108-0.036-0.06840.037-0.107317.2656-27.63850.6876
291.07190.30030.71331.07211.01221.4998-0.09410.1023-0.2124-0.01140.0164-0.0240.2813-0.18020.0777-0.0974-0.17020.0025-0.1524-0.072-0.028413.0233-57.952348.8354
300.0986-0.4071-0.15831.7860.11343.04130.0734-0.02670.16040.0802-0.04560.0629-0.356-0.2433-0.02780.01140.0790.0752-0.1692-0.0053-0.126919.6055-1.940176.3294
310.6645-0.06970.30280.0824-0.0920.76950.0277-0.0873-0.16120.04730.0260.0441-0.072-0.1393-0.0538-0.1355-0.04090.0335-0.06380.0771-0.108117.8455-30.664182.0166
321.69280.58631.33162.21790.23722.2320.32550.059-0.55150.10390.0388-0.02340.6604-0.0273-0.36430.0017-0.064-0.0678-0.29260.05730.075524.6719-60.251376.1042
331.91750.2793-1.24521.7734-0.95651.15530.1324-0.3160.10370.1721-0.2589-0.2403-0.5680.23890.12650.0506-0.2789-0.0821-0.05040.004-0.162262.7277-1.455485.0634
340.4363-0.1705-0.05080.7261-0.11660.79730.0585-0.2352-0.0773-0.0202-0.2027-0.0872-0.08370.3180.1442-0.2427-0.1091-0.03440.14790.2306-0.130375.9666-27.629680.2269
351.58170.10620.68744.48760.30033.120.0498-0.2823-0.6634-0.1607-0.3049-0.06960.89840.82610.2551-0.22420.27530.0963-0.00210.37370.138284.5992-56.825375.8877
362.20550.3793-0.63250.2831-0.40852.48070.14650.07350.153-0.0132-0.08980.0249-0.44430.0616-0.05670.0506-0.0230.0183-0.23280.1406-0.061248.36454.51343.308
370.48260.1066-0.23750.3222-0.11250.2117-0.02660.1247-0.0439-0.0322-0.0508-0.03220.0011-0.02350.0774-0.0561-0.01280.0108-0.08520.0618-0.144344.7042-22.63432.3808
380.9298-0.3250.53771.28360.00040.3853-0.14920.1569-0.3325-0.21220.0733-0.11870.331-0.07320.0760.0474-0.02120.096-0.2205-0.1043-0.042845.8-53.369434.4837
390.8146-3.5988-0.407118.80722.99661.1971-0.01630.1009-0.03980.7548-0.13570.06530.3-0.0210.152-0.0223-0.04940.0671-0.17530.0541-0.11151.386-48.483864.5239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 95
2X-RAY DIFFRACTION2A96 - 379
3X-RAY DIFFRACTION2A600 - 700
4X-RAY DIFFRACTION3A380 - 510
5X-RAY DIFFRACTION4B23 - 95
6X-RAY DIFFRACTION5B96 - 379
7X-RAY DIFFRACTION5B600 - 700
8X-RAY DIFFRACTION6B380 - 509
9X-RAY DIFFRACTION7C16 - 95
10X-RAY DIFFRACTION8C96 - 379
11X-RAY DIFFRACTION8C600 - 700
12X-RAY DIFFRACTION9C380 - 510
13X-RAY DIFFRACTION10D9 - 82
14X-RAY DIFFRACTION11D83 - 363
15X-RAY DIFFRACTION11D600 - 700
16X-RAY DIFFRACTION12D364 - 475
17X-RAY DIFFRACTION13E9 - 82
18X-RAY DIFFRACTION14E83 - 363
19X-RAY DIFFRACTION14E602
20X-RAY DIFFRACTION15E364 - 474
21X-RAY DIFFRACTION16F9 - 82
22X-RAY DIFFRACTION17F83 - 363
23X-RAY DIFFRACTION17F600 - 700
24X-RAY DIFFRACTION18F364 - 474
25X-RAY DIFFRACTION19G1 - 30
26X-RAY DIFFRACTION19G220 - 272
27X-RAY DIFFRACTION20G31 - 219
28X-RAY DIFFRACTION21H24 - 95
29X-RAY DIFFRACTION22H96 - 379
30X-RAY DIFFRACTION22H600 - 700
31X-RAY DIFFRACTION23H380 - 510
32X-RAY DIFFRACTION24I23 - 95
33X-RAY DIFFRACTION25I96 - 379
34X-RAY DIFFRACTION25I600 - 700
35X-RAY DIFFRACTION26I380 - 509
36X-RAY DIFFRACTION27J16 - 95
37X-RAY DIFFRACTION28J96 - 379
38X-RAY DIFFRACTION28J600 - 700
39X-RAY DIFFRACTION29J380 - 510
40X-RAY DIFFRACTION30K9 - 82
41X-RAY DIFFRACTION31K83 - 363
42X-RAY DIFFRACTION31K600 - 700
43X-RAY DIFFRACTION32K364 - 475
44X-RAY DIFFRACTION33L9 - 82
45X-RAY DIFFRACTION34L83 - 363
46X-RAY DIFFRACTION34L602
47X-RAY DIFFRACTION35L364 - 474
48X-RAY DIFFRACTION36M9 - 82
49X-RAY DIFFRACTION37M83 - 363
50X-RAY DIFFRACTION37M600 - 700
51X-RAY DIFFRACTION38M364 - 474
52X-RAY DIFFRACTION39N1 - 30
53X-RAY DIFFRACTION39N220 - 272

+
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