[English] 日本語
Yorodumi
- PDB-3zia: The structure of F1-ATPase from Saccharomyces cerevisiae inhibite... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zia
TitleThe structure of F1-ATPase from Saccharomyces cerevisiae inhibited by its regulatory protein IF1
Components
  • (ATP SYNTHASE SUBUNIT ...) x 5
  • ATPASE INHIBITOR, MITOCHONDRIAL
KeywordsHYDROLASE / NATURAL INHIBITOR / CATALYSIS / INTERMEDIATE
Function / homology
Function and homology information


: / : / Mitochondrial protein degradation / ATPase inhibitor activity / enzyme inhibitor activity / molecular function inhibitor activity / proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis ...: / : / Mitochondrial protein degradation / ATPase inhibitor activity / enzyme inhibitor activity / molecular function inhibitor activity / proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / : / 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, 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 / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / Lysin / Thrombin, subunit H - #170 ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / 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 / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / Lysin / Thrombin, subunit H - #170 / 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, 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, F1 complex, alpha subunit nucleotide-binding domain / 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. / 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 / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / F(1)-ATPase inhibitor IF(1), 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: 2.5 Å
AuthorsRobinson, G.C. / Bason, J.V. / Montgomery, M.G. / Fearnley, I.M. / Mueller, D.M. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Open Biol. / Year: 2013
Title: The Structure of F1-ATPase from Saccharomyces Cerevisiae Inhibited by its Regulatory Protein If1.
Authors: Robinson, G.C. / Bason, J.V. / Montgomery, M.G. / Fearnley, I.M. / Mueller, D.M. / Leslie, A.G.W. / Walker, J.E.
History
DepositionJan 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Dec 20, 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_sheet / 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_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.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_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_sheet.number_strands / _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 19-STRANDED BARREL THIS IS REPRESENTED BY A 20-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 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 19-STRANDED BARREL THIS IS REPRESENTED BY A 20-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
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
J: ATPASE INHIBITOR, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
T: ATPASE INHIBITOR, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)761,39748
Polymers755,49520
Non-polymers5,90228
Water13,926773
1
K: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
T: ATPASE INHIBITOR, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,82326
Polymers377,74810
Non-polymers3,07516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48000 Å2
ΔGint-225.8 kcal/mol
Surface area115970 Å2
MethodPISA
2
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
J: ATPASE INHIBITOR, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,57422
Polymers377,74810
Non-polymers2,82712
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47000 Å2
ΔGint-245.5 kcal/mol
Surface area116140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.224, 187.846, 181.812
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21K
12B
22L
13C
23M
14D
24N
15F
25P
16G
26Q
17H
27R
18I
28S
19J
29T
110E
210O

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A26 - 700
2111K26 - 700
1121B25 - 700
2121L25 - 700
1131C26 - 700
2131M26 - 700
1141D6 - 700
2141N6 - 700
1151F7 - 700
2151P7 - 700
1161G1 - 276
2161Q1 - 276
1171H11 - 137
2171R11 - 137
1181I1 - 61
2181S1 - 61
1191J1 - 36
2191T1 - 36
11101E8 - 700
21101O8 - 700

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
Components

-
ATP SYNTHASE SUBUNIT ... , 5 types, 18 molecules ABCKLMDEFNOPGQHRIS

#1: Protein
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL / F1-ATPASE


Mass: 55007.402 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: W303-1A / References: UniProt: P07251
#2: Protein
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL / F1-ATPASE


Mass: 51181.082 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: W303-A1
References: UniProt: P00830, H+-transporting two-sector ATPase
#3: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / F-ATPASE GAMMA SUBUNIT / F1-ATPASE


Mass: 30657.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: W303-1A / References: UniProt: P38077
#4: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / F-ATPASE DELTA SUBUNIT / F1-ATPASE


Mass: 14565.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: W303-1A / References: UniProt: Q12165
#5: Protein ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / ATPASE SUBUNIT EPSILON / F1-ATPASE


Mass: 6618.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: W303-1A / References: UniProt: P21306

-
Protein , 1 types, 2 molecules JT

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


Mass: 7341.197 Da / Num. of mol.: 2 / Fragment: INHIBITOR PROTEIN, UNP RESIDUES 23-75 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303-A1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P01097

-
Non-polymers , 5 types, 801 molecules

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


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 10 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.72 % / Description: NONE
Crystal growTemperature: 296 K / Method: microbatch / pH: 7.5
Details: ACTIVE F1-ATPASE (12 MG/ML) WAS EXCHANGED ON A DESALTING COLUMN INTO CRYSTALLISATION BUFFER, PREPARED IN D2O CONSISTING OF 100 MM BIS-TRIS PROPANE, PH 7.5, 100 MM SUCROSE, 1 MM ADP AND 10 MM ...Details: ACTIVE F1-ATPASE (12 MG/ML) WAS EXCHANGED ON A DESALTING COLUMN INTO CRYSTALLISATION BUFFER, PREPARED IN D2O CONSISTING OF 100 MM BIS-TRIS PROPANE, PH 7.5, 100 MM SUCROSE, 1 MM ADP AND 10 MM MAGNESIUM SULPHATE. THEN THE ENZYME WAS INHIBITED AT 23C WITH A 4-FOLD MOLAR EXCESS OF YI1-53 (MUTATION E21A) IN THE PRESENCE OF 1 MM ATP AND 2 MM MAGNESIUM SULPHATE. FURTHER PORTIONS (5 UL OF A NEUTRALISED STOCK SOLUTION CONTAINING 200 MM ATP AND 400 MM MAGNESIUM SULPHATE/ML PROTEIN SOLUTION) WERE ADDED AFTER 5 AND 10 MIN. MORE THAN 95% OF THE ATP HYDROLYSIS ACTIVITY OF THE ENZYME WAS INHIBITED. SODIUM-POTASSIUM TARTRATE WAS ADDED TO 100 MM, AND THE CONCENTRATION OF THE PROTEIN SOLUTION WAS ADJUSTED TO 10 MG/ML WITH CRYSTALLISATION BUFFER. CRYSTALS WERE GROWN AT 23C IN 72 WELL MICRO-BATCH PLATES UNDER FILTERED PARAFFIN OIL. THE CRYSTALLISATION DROPS (4 UL) CONTAINED A 1:1 MIXTURE OF PROTEIN SOLUTION AND PRECIPITANT SOLUTION (20%-26% POLYETHYLENE GLYCOL 3000 AND 600 MM NACL PREPARED IN D2O).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.977
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.5→43.84 Å / Num. obs: 268620 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HLD

2hld


Resolution: 2.5→181.81 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.398 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.601 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26194 13570 5.1 %RANDOM
Rwork0.2243 ---
obs0.22618 254974 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.46 Å2
2--0.66 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.5→181.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50724 0 366 773 51863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02251972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9970394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47256662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08224.5262152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.365159064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.40915344
X-RAY DIFFRACTIONr_chiral_restr0.0750.28250
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02138480
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_it0.5761.533069
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.084253182
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.688518903
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.592817205
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

Dom-ID: 2 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1K3715tight positional0.010.02
2L3687tight positional0.010.02
3M3712tight positional0.010.02
4N3581tight positional0.010.02
5P3569tight positional0.010.02
6Q2051tight positional0.010.02
7R937tight positional00.02
8S450tight positional00.02
9T283tight positional00.02
10O3563tight positional0.010.02
1K3715tight thermal3.310
2L3687tight thermal6.410
3M3712tight thermal3.8110
4N3581tight thermal2.5710
5P3569tight thermal3.3510
6Q2051tight thermal5.1610
7R937tight thermal0.7810
8S450tight thermal2.2210
9T283tight thermal2.1810
10O3563tight thermal6.8210
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 996 -
Rwork0.335 18559 -
obs--96.87 %

+
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