[English] 日本語
Yorodumi
- PDB-4ayb: RNAP at 3.2Ang -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ayb
TitleRNAP at 3.2Ang
Components(DNA-DIRECTED RNA ...) x 13
KeywordsTRANSFERASE / MULTI-SUBUNIT / TRANSCRIPTION
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleic acid binding / molecular adaptor activity / protein dimerization activity ...3 iron, 4 sulfur cluster binding / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleic acid binding / molecular adaptor activity / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
DNA Excision Repair, Uvrb; Chain A - #10 / DNA Excision Repair, Uvrb; Chain A / Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / RNA polymerase Rpo13 subunit HTH domain ...DNA Excision Repair, Uvrb; Chain A - #10 / DNA Excision Repair, Uvrb; Chain A / Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / Dihydrolipoamide Transferase / HRDC domain / RNA polymerase ii / RNA polymerase Rpb1 funnel domain / N-terminal domain of TfIIb / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Other non-globular / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, domain 2 / Helix Hairpins / S1 domain profile. / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / Helix non-globular / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 ...IRON/SULFUR CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13
Similarity search - Component
Biological speciesSULFOLOBUS SHIBATAE (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.202 Å
AuthorsWojtas, M.N. / Mogni, M. / Millet, O. / Bell, S.D. / Abrescia, N.G.A.
Citation
Journal: Nucleic Acids Res. / Year: 2012
Title: Structural and Functional Analyses of the Interaction of Archaeal RNA Polymerase with DNA.
Authors: Wojtas, M.N. / Mogni, M. / Millet, O. / Bell, S.D. / Abrescia, N.G.A.
#1: Journal: Biochem.Soc.Trans. / Year: 2011
Title: Archaeal RNA Polymerase: The Influence of the Protruding Stalk in Crystal Packing and Preliminary Biophysical Analysis of the Rpo13 Subunit.
Authors: Wojtas, M. / Peralta, B. / Ondiviela, M. / Mogni, M. / Bell, S.D. / Abrescia, N.G.A.
#2: Journal: Plos Biol. / Year: 2009
Title: Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
Authors: Korkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.
History
DepositionJun 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2Sep 5, 2012Group: Atomic model
Revision 1.3Nov 7, 2012Group: Database references
Revision 1.4Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.5Dec 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BQ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE
B: DNA-DIRECTED RNA POLYMERASE
C: DNA-DIRECTED RNA POLYMERASE
D: DNA-DIRECTED RNA POLYMERASE
E: DNA-DIRECTED RNA POLYMERASE
F: DNA-DIRECTED RNA POLYMERASE
G: DNA-DIRECTED RNA POLYMERASE
H: DNA-DIRECTED RNA POLYMERASE
K: DNA-DIRECTED RNA POLYMERASE
L: DNA-DIRECTED RNA POLYMERASE
N: DNA-DIRECTED RNA POLYMERASE
P: DNA-DIRECTED RNA POLYMERASE
Q: DNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,66625
Polymers405,63613
Non-polymers1,03012
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74780 Å2
ΔGint-334.1 kcal/mol
Surface area162090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.725, 212.415, 128.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
DNA-DIRECTED RNA ... , 13 types, 13 molecules ABCDEFGHKLNPQ

#1: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 99766.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO1N SUBUNIT / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB53, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 127582.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO2 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB55, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 43792.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO1C / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB54, DNA-directed RNA polymerase
#4: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 30179.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO3 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB56, DNA-directed RNA polymerase
#5: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 20328.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO7 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB57, DNA-directed RNA polymerase
#6: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 12822.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPOF / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB58, DNA-directed RNA polymerase
#7: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 15139.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO8 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB59, DNA-directed RNA polymerase
#8: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 9688.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO5 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB60, DNA-directed RNA polymerase
#9: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 10729.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO6 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB61, DNA-directed RNA polymerase
#10: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 10211.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO11 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB62, DNA-directed RNA polymerase
#11: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 7617.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO10 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB63, DNA-directed RNA polymerase
#12: Protein/peptide DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 5606.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO12 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB64, DNA-directed RNA polymerase
#13: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 12170.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RPO13 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB65, DNA-directed RNA polymerase

-
Non-polymers , 3 types, 12 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 % / Description: NONE

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→40.1 Å / Num. obs: 88449 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 13.9
Reflection shellResolution: 3.2→3.27 Å / Redundancy: 15.3 % / Mean I/σ(I) obs: 2 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WAQ

2waq


Resolution: 3.202→40.097 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 30.23 / Stereochemistry target values: ML / Details: THIS ENTRY UPDATES PDB ENTRIES 2WAQ AND 2WB1.
RfactorNum. reflection% reflection
Rfree0.3005 4426 5 %
Rwork0.2425 --
obs0.2454 88375 99.43 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.52 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 95.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.1928 Å20 Å20 Å2
2---12.2327 Å20 Å2
3---3.0399 Å2
Refinement stepCycle: LAST / Resolution: 3.202→40.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27103 0 18 0 27121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727638
X-RAY DIFFRACTIONf_angle_d0.76237329
X-RAY DIFFRACTIONf_dihedral_angle_d12.61210602
X-RAY DIFFRACTIONf_chiral_restr0.0444243
X-RAY DIFFRACTIONf_plane_restr0.0044781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2021-3.27650.39272910.3275398X-RAY DIFFRACTION97
3.2765-3.35840.35972900.31445540X-RAY DIFFRACTION99
3.3584-3.44920.37542890.30735524X-RAY DIFFRACTION99
3.4492-3.55060.33413100.28155544X-RAY DIFFRACTION99
3.5506-3.66520.31172710.27155531X-RAY DIFFRACTION99
3.6652-3.79610.31112890.25665578X-RAY DIFFRACTION100
3.7961-3.94790.32512780.24545553X-RAY DIFFRACTION100
3.9479-4.12740.31483260.2385540X-RAY DIFFRACTION100
4.1274-4.34480.31692870.21785590X-RAY DIFFRACTION100
4.3448-4.61660.24622980.19445591X-RAY DIFFRACTION100
4.6166-4.97250.25072780.20135644X-RAY DIFFRACTION100
4.9725-5.47180.2943130.23215612X-RAY DIFFRACTION100
5.4718-6.2610.31972810.25195695X-RAY DIFFRACTION100
6.261-7.87830.28753060.22795718X-RAY DIFFRACTION100
7.8783-40.09980.27153190.23735891X-RAY DIFFRACTION99
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)
12.4592-0.26010.02153.2027-0.41353.3510.42260.3210.4668-0.7344-0.07110.1982-0.9356-0.36550.01730.78050.2877-0.14660.56770.03990.044-58.072330.7049-41.0023
21.6291-0.16270.34212.16610.16731.6725-0.03420.0668-0.16110.51130.0477-0.1890.14880.1319-0.0014-0.17760.2087-0.0686-0.12890.041-0.0368-38.097311.40111.591
30.64920.68370.61230.88910.78230.7636-0.11520.2080.3585-0.21580.0696-0.0538-0.18230.2308-0.01670.20130.11320.05090.3107-0.02560.514-26.1420.1813-1.9669
41.5098-0.64020.99622.7621-1.21882.2976-0.11420.11480.52730.3314-0.0355-0.1112-0.4912-0.0637-0.00010.17870.02790.0138-0.0037-0.03430.4189-52.666367.81244.6378
50.82580.32630.4041.29780.32291.66790.19160.69270.1772-0.6071-0.0746-0.0794-0.12490.0239-00.50280.02940.18850.75610.39340.8126-23.902564.571-25.9886
60.737-0.27930.0741.6074-0.0560.8006-0.0580.19350.64730.24890.0120.0396-0.3031-0.0520.0278-0.11710.0984-0.0752-0.043-0.0175-0.2355-45.620643.10766.3882
71.80350.01820.71630.6722-0.19752.38310.21020.2387-0.149-0.09560.0321-0.65420.30090.3946-0.00080.04780.09430.01090.3829-0.17390.3812-22.4445-3.3751-7.4783
81.32420.1052-0.48661.22791.02311.16460.01750.2152-0.0728-0.6667-0.02010.3311-0.18030.0755-0.00010.2787-0.2064-0.04671.0533-0.01570.98341.900837.8921-29.475
91.6073-0.07060.18260.899-0.05121.8483-0.02420.61890.1793-0.57460.0868-0.2809-0.18260.2016-0.01480.10180.02410.01960.392-0.03330.3717-32.301311.5001-22.6627
102.27790.04460.15081.69450.0521.73290.1054-0.6254-0.0830.61410.08820.58890.0885-0.53480.00820.88240.22830.29610.61550.0440.1483-65.048627.672142.819
111.0852-0.9403-0.62692.0621-0.21461.3441-0.2149-0.5748-0.1141.01380.279-0.1639-0.14270.14630.00811.29820.197-0.18230.56250.12350.0387-38.472615.065149.788
120.8824-0.2011-0.19880.6531-0.17630.59270.09550.9959-0.1914-0.4991-0.20390.46070.3335-0.3252-0.01140.24660.0048-0.22410.5072-0.2050.6852-73.5684-14.2971-26.5944
130.02810.06270.05590.14180.1290.115-0.57731.0798-0.3735-0.27070.05780.54510.7843-1.1416-0.00011.0733-0.0118-0.18162.4034-0.1751.2937-99.3394-11.1045-54.9424
140.030.0707-0.05760.1551-0.13790.11450.10850.2383-0.347-0.94460.51530.73230.6054-0.44690.00030.8083-0.1414-0.52831.39370.07361.4207-85.2196-21.54-38.0025
150.0772-0.02370.07960.0063-0.02260.07830.54850.1388-0.222-0.70160.58790.59860.039-0.69070.00011.70820.2103-0.34572.0888-0.77141.8279-80.4496-26.4188-57.7583
161.03240.1866-0.06130.5512-0.31240.7288-0.1647-0.655-0.37740.75840.1167-0.83510.39860.56410.00480.95080.1927-0.37120.62760.1370.4682-13.8804-10.914235.559
170.9511-0.1364-0.05560.9584-0.19221.0545-0.17680.7894-0.0969-0.6380.1303-0.5929-0.03960.2572-0.00690.42730.17270.04620.651-0.16120.5182-23.1702-1.7332-31.6842
182.4175-0.63520.87941.9677-0.64341.6971-0.1604-0.1208-0.74490.14210.0320.06020.55520.1146-0.04120.2343-0.0657-0.13160.1229-0.04950.4734-51.2796-12.769-8.3443
191.32850.2725-0.04110.5635-0.51280.5472-0.0294-0.2733-0.65180.17660.26510.12350.2289-0.34350.00020.91710.04690.00770.46860.28610.3227-53.134-2.52538.4677
200.2436-0.5018-0.1871.9571-0.46690.9288-0.5916-0.38630.08161.49160.74470.1441-0.6635-0.51110.09870.86730.25760.02520.3671-0.24220.0553-50.535941.780939.7178
210.3796-0.00970.02230.38650.28170.72860.1188-0.34080.47250.52610.11810.5596-0.5488-0.0728-0.00740.54620.35970.28220.41010.0180.6592-79.44650.928919.5126
220.1661-0.15980.01180.1696-0.06640.17970.11970.73350.56-0.89360.4251-0.8645-0.21830.26970.00021.19610.10270.16791.4748-0.36910.8081-29.5532-1.4839-48.8604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 3:298
2X-RAY DIFFRACTION2CHAIN A AND RESID 299:755
3X-RAY DIFFRACTION3CHAIN A AND RESID 756:879
4X-RAY DIFFRACTION4CHAIN B AND RESID 7:174
5X-RAY DIFFRACTION5CHAIN B AND RESID 175:334
6X-RAY DIFFRACTION6CHAIN B AND RESID 335:1125
7X-RAY DIFFRACTION7CHAIN C AND RESID 7:125
8X-RAY DIFFRACTION8CHAIN C AND RESID 126:249
9X-RAY DIFFRACTION9CHAIN C AND RESID 250:395
10X-RAY DIFFRACTION10CHAIN D AND RESID 2:157
11X-RAY DIFFRACTION11CHAIN D AND RESID 158:263
12X-RAY DIFFRACTION12CHAIN E AND RESID 1:78
13X-RAY DIFFRACTION13CHAIN E AND RESID 79:177
14X-RAY DIFFRACTION14CHAIN F AND RESID 3:46
15X-RAY DIFFRACTION15CHAIN F AND RESID 47:110
16X-RAY DIFFRACTION16CHAIN G
17X-RAY DIFFRACTION17CHAIN H
18X-RAY DIFFRACTION18CHAIN K
19X-RAY DIFFRACTION19CHAIN L
20X-RAY DIFFRACTION20CHAIN N
21X-RAY DIFFRACTION21CHAIN P
22X-RAY DIFFRACTION22CHAIN Q

+
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