[English] 日本語
Yorodumi
- PDB-2v7q: The structure of F1-ATPase inhibited by I1-60HIS, a monomeric for... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v7q
TitleThe structure of F1-ATPase inhibited by I1-60HIS, a monomeric form of the inhibitor protein, IF1.
Components
  • (ATP SYNTHASE ...) x 5
  • ATPASE INHIBITOR
KeywordsHYDROLASE / ION TRANSPORT / MITOCHONDRION / TRANSIT PEPTIDE / INHIBITOR PROTEIN
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / Mitochondrial protein degradation ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single helix bin / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / 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 Epsilon Chain; Chain: I; / ATP synthase alpha/beta chain, C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP ...Single helix bin / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / 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 Epsilon Chain; Chain: I; / ATP synthase alpha/beta chain, C-terminal domain / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / Lysin / Thrombin, subunit H - #170 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 - #20 / 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 / Pyruvate Kinase; Chain: A, domain 1 / 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, alpha subunit nucleotide-binding domain / 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 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 / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: How the Regulatory Protein, If1, Inhibits F1- ATPase from Bovine Mitochondria.
Authors: Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
History
DepositionJul 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 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
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
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 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 DELTA CHAIN
I: ATP SYNTHASE EPSILON CHAIN
J: ATPASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,24821
Polymers379,65510
Non-polymers2,59211
Water34,9491940
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47950 Å2
ΔGint-230.6 kcal/mol
Surface area144720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.534, 103.271, 135.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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

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


Mass: 55332.219 Da / Num. of mol.: 3 / Fragment: RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE
References: UniProt: Q1JQC4, UniProt: P19483*PLUS, EC: 3.6.1.14
#2: Protein ATP SYNTHASE SUBUNIT BETA / ATP SYNTHASE BETA CHAIN


Mass: 51757.836 Da / Num. of mol.: 3 / Fragment: RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.14
#3: Protein ATP SYNTHASE GAMMA CHAIN / ATP SYNTHASE GAMMA SUBUNIT


Mass: 30185.674 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-297 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34
#4: Protein ATP SYNTHASE DELTA CHAIN / ATP SYNTHASE DELTA SUBUNIT


Mass: 15074.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-168 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05630, EC: 3.6.1.14
#5: Protein/peptide ATP SYNTHASE EPSILON CHAIN / ATP SYNTHASE EPSILON SUBUNIT


Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05632, EC: 3.6.1.14

-
Protein , 1 types, 1 molecules J

#6: Protein ATPASE INHIBITOR / BOVINE MITOCHONDRIAL F1-ATPASE INHIBITOR PROTEIN


Mass: 7462.098 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Tissue: MUSCLE / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01096

-
Non-polymers , 5 types, 1951 molecules

#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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.: 1940 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsI1-60HIS IS A TRUNCATED FRAGMENT OF THE BOVINE ATPASE INHIBITOR PROTEIN. RESIDUES 1-60 PLUS 6 C- ...I1-60HIS IS A TRUNCATED FRAGMENT OF THE BOVINE ATPASE INHIBITOR PROTEIN. RESIDUES 1-60 PLUS 6 C-TERMINAL HISTIDINES

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.21 % / Description: NONE
Crystal growpH: 8.2 / Details: pH 8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→69.7 Å / Num. obs: 212416 / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 97.7

-
Processing

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

1ohh


Resolution: 2.1→37.19 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.233 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 10665 5 %RANDOM
Rwork0.19 ---
obs0.193 201634 99 %-
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: 41.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å20 Å2
2---1.19 Å20 Å2
3---3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25321 0 157 1940 27418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02225875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.221.98734986
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34453308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16524.2051075
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62154581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.15615187
X-RAY DIFFRACTIONr_chiral_restr0.0810.24074
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219107
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.212301
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.217841
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.22050
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.329316952
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.117526419
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5879939
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.114108562
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 728
Rwork0.227 14277
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)
12.2828-0.49970.75172.06560.21413.6564-0.07430.04340.26350.06470.0611-0.1434-0.2070.18510.0131-0.0566-0.0133-0.0515-0.0486-0.0003-0.0919138.64639.444510.7341
20.8711-0.1331-0.23330.5633-0.40131.3481-0.0441-0.12850.11820.0990.04310.0612-0.037-0.04790.0009-0.00270.00680.0042-0.0948-0.0364-0.0921110.704146.341521.3246
35.39320.8695-0.24514.38810.35451.81020.0451-0.45750.54550.4082-0.01830.8193-0.0687-0.6037-0.0269-0.16960.05670.16650.0857-0.06060.005981.16252.770528.701
42.02720.0469-0.42653.18791.1291.860.0163-0.1203-0.08680.17560.0395-0.11570.09290.0992-0.0558-0.03870.0495-0.0128-0.0520.0391-0.1071135.0199-2.057112.8418
50.72260.1413-0.07031.40440.05730.66730.0113-0.0905-0.08190.1594-0.02920.16170.0821-0.05510.0179-0.00870.02080.0489-0.07310.0516-0.068105.6848-10.588412.8718
64.19560.8294-1.50655.5583-0.95633.2522-0.04040.3095-0.3529-0.0359-0.02121.34850.1779-0.64430.0617-0.2805-0.06630.1924-0.0808-0.12770.37475.8119-16.734513.8062
72.3066-0.23480.14062.4988-0.8072.58820.00950.188-0.2334-0.00790.02770.02820.0420.0383-0.0372-0.10950.00070.02790.0549-0.053-0.1395135.423616.736-24.4997
80.8911-0.3001-0.11741.50020.19580.4528-0.00840.19030.035-0.2644-0.04630.2433-0.0320.01210.0547-0.0574-0.0172-0.06350.00130.0178-0.0772106.577725.5145-30.5418
94.02140.3550.04442.94930.87593.3894-0.08720.17890.2087-0.14980.09370.8517-0.0832-0.6419-0.0065-0.18840.0339-0.2720.03160.01460.300176.200529.6639-34.3755
100.8787-0.2556-0.1412.14930.15531.97130.00060.09520.0768-0.00460.0521-0.171-0.1360.1853-0.0528-0.0875-0.0396-0.00520.00870.0005-0.075136.833838.7-15.4815
110.8155-0.1436-0.06450.42660.0330.4905-0.030.1380.1551-0.00690.01960.0483-0.06380.01630.0104-0.0254-0.0227-0.0165-0.06670.0698-0.0393110.519451.5018-11.8904
122.17850.3614-0.04871.1751-0.14940.7404-0.0660.22110.145-0.08610.0270.435-0.1825-0.20480.039-0.09760.0655-0.0767-0.08170.05520.079279.64851.6288-7.7982
131.67060.5244-0.48742.1075-0.03521.7439-0.0837-0.1705-0.12550.2335-0.0199-0.13470.06020.12210.1036-0.01260.0584-0.0525-0.01690.0029-0.1224136.06421.038525.2549
140.8549-0.09570.02931.24170.31080.8518-0.0774-0.2485-0.06220.28460.0180.22390.0469-0.13120.05940.00640.04110.08080.01220.0376-0.0938108.382715.564635.025
1513.40240.4487-0.60141.3070.51632.3778-0.0762-0.48050.1856-0.06550.14120.6206-0.3514-0.6689-0.065-0.05860.05810.3019-0.07770.10420.005278.145114.278640.7009
161.63490.89090.37911.512-0.68832.5030.00330.1066-0.1686-0.00780.031-0.0780.10370.2134-0.0343-0.06450.0610.0459-0.0102-0.0159-0.0828133.7519-5.5075-10.7222
170.6887-0.0575-0.03131.57480.18370.32030.00750.1081-0.0446-0.0126-0.04870.23330.1227-0.03760.0412-0.0603-0.0120.0205-0.0443-0.0137-0.0495105.3235-5.7924-18.641
180.961-1.0128-0.40363.01060.84381.7434-0.1650.1472-0.48320.2486-0.2271.10750.1124-0.44680.392-0.2973-0.07380.0772-0.0983-0.18520.506775.76211.9843-14.6179
1911.7138-2.1464-1.53950.55410.40030.7181-0.0027-0.14280.15540.13130.01330.1078-0.0055-0.0456-0.0106-0.0970.0140.073-0.1250.05350.053187.137322.69436.2944
205.5342-0.1733-1.31082.14750.70352.4676-0.0080.9042-0.3098-0.26940.03440.1369-0.0685-0.7809-0.0265-0.22890.02730.14490.2885-0.10450.002244.104326.6609-0.1327
219.02970.498-3.32573.68490.63116.00640.12230.0055-0.1386-0.0631-0.0338-0.00490.1361-0.3914-0.0885-0.24050.1130.11140.1064-0.0211-0.106728.95231.944719.2857
225.6765-0.48814.40337.26832.05915.9251-0.40390.07320.9281-0.59780.28340.5239-1.56490.36680.12050.03560.03550.19240.0392-0.09580.057435.889554.168714.6789
233.250.73210.37183.0277.429618.8960.15140.79030.498-0.95560.21660.2467-2.4371-0.2453-0.36810.09230.15280.20940.05270.12170.057535.899146.21697.7481
2411.7888-4.7329-34.25226.54422.9968121.07790.1090.17370.9971-0.7538-1.93650.1214-4.79350.24761.8275-0.0018-0.00120.00130.00120.0009-0.000251.639642.212810.0609
257.21011.4528-3.77088.44822.681111.43510.2179-0.02540.22240.41280.007-0.2589-0.35970.6694-0.22490.07530.01780.00850.08730.10110.262787.215433.22843.4972
2611.1979-11.62376.696415.1358-7.89425.3075-0.06960.20230.0497-0.1270.00040.29770.1419-0.22470.06920.05370.007-0.07020.2301-0.02130.42669.101142.6475-11.6685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 95
2X-RAY DIFFRACTION2A96 - 379
3X-RAY DIFFRACTION2A1511 - 1512
4X-RAY DIFFRACTION3A380 - 510
5X-RAY DIFFRACTION4B24 - 95
6X-RAY DIFFRACTION5B96 - 379
7X-RAY DIFFRACTION5B1511 - 1512
8X-RAY DIFFRACTION6B380 - 510
9X-RAY DIFFRACTION7C23 - 95
10X-RAY DIFFRACTION8C96 - 379
11X-RAY DIFFRACTION8C1511 - 1512
12X-RAY DIFFRACTION9C380 - 510
13X-RAY DIFFRACTION10D9 - 82
14X-RAY DIFFRACTION11D83 - 363
15X-RAY DIFFRACTION11D1478 - 1479
16X-RAY DIFFRACTION12D364 - 477
17X-RAY DIFFRACTION13E10 - 82
18X-RAY DIFFRACTION14E83 - 363
19X-RAY DIFFRACTION15E364 - 474
20X-RAY DIFFRACTION16F9 - 82
21X-RAY DIFFRACTION17F83 - 363
22X-RAY DIFFRACTION17F1475 - 1476
23X-RAY DIFFRACTION18F364 - 474
24X-RAY DIFFRACTION19G1 - 30
25X-RAY DIFFRACTION19G220 - 272
26X-RAY DIFFRACTION20G31 - 219
27X-RAY DIFFRACTION21H15 - 97
28X-RAY DIFFRACTION22H98 - 145
29X-RAY DIFFRACTION23I1 - 27
30X-RAY DIFFRACTION24I28 - 47
31X-RAY DIFFRACTION25J8 - 20
32X-RAY DIFFRACTION26J21 - 50

+
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