[English] 日本語
Yorodumi
- PDB-3k1f: Crystal structure of RNA Polymerase II in complex with TFIIB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k1f
TitleCrystal structure of RNA Polymerase II in complex with TFIIB
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Transcription initiation factor IIB
KeywordsTRANSCRIPTION / RNA Polymerase II / TFIIB / Transcription Factor / Transcription Initiation / DNA-binding / DNA-directed RNA polymerase / Isopeptide bond / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Zinc-finger / DNA damage / DNA repair / mRNA processing / Initiation factor
Function / homology
Function and homology information


: / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II general transcription initiation factor activity ...: / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II general transcription initiation factor activity / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / Estrogen-dependent gene expression / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Gap-filling DNA repair synthesis and ligation in TC-NER / termination of RNA polymerase II transcription / Dual incision in TC-NER / termination of RNA polymerase I transcription / transcription by RNA polymerase III / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / positive regulation of translational initiation / nuclear-transcribed mRNA catabolic process / RNA polymerase II preinitiation complex assembly / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor activity / transcription-coupled nucleotide-excision repair / translation initiation factor binding / TBP-class protein binding / translesion synthesis / DNA-templated transcription elongation / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / P-body / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / transcription by RNA polymerase II / ribonucleoside binding / mRNA processing / cytoplasmic stress granule / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / peroxisome / single-stranded DNA binding / ribosome biogenesis / nucleic acid binding / protein dimerization activity / single-stranded RNA binding / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / nucleoplasm / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / DNA-directed RNA polymerase II subunit Rpb4-like / Cyclin-like ...Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / DNA-directed RNA polymerase II subunit Rpb4-like / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / Cyclin-like superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / : / DNA-directed RNA polymerase, subunit RPB6 / 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. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / Zinc finger, TFIIS-type / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit CX / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain
Similarity search - Domain/homology
Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 ...Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsKostrewa, D. / Zeller, M.E. / Armache, K.-J. / Seizl, M. / Leike, K. / Thomm, M. / Cramer, P.
CitationJournal: Nature / Year: 2009
Title: RNA polymerase II-TFIIB structure and mechanism of transcription initiation.
Authors: Kostrewa, D. / Zeller, M.E. / Armache, K.J. / Seizl, M. / Leike, K. / Thomm, M. / Cramer, P.
History
DepositionSep 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2013Group: Other
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,43822
Polymers532,85013
Non-polymers5899
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74640 Å2
ΔGint-325 kcal/mol
Surface area155330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.97, 408.27, 275.24
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / DNA-directed RNA polymerase II 140 kDa polypeptide / B150


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa ...RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa polypeptide / B44.5


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II 32 kDa polypeptide / B32


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34087, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / B12.6


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27999, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.6 kDa polypeptide / B13.6


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38902, DNA-directed RNA polymerase

-
DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 kDa polypeptide / ABC27


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 kDa polypeptide / ABC23


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 kDa polypeptide / ABC14.5 / ABC14.4


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 kDa polypeptide / ABC10-beta / ABC8


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139, DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422, DNA-directed RNA polymerase

-
Protein / Non-polymers , 2 types, 10 molecules M

#13: Protein Transcription initiation factor IIB


Mass: 18691.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B3LK56, UniProt: P29055*PLUS
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

-
Details

Sequence detailsTHE B-LINKER AND B-CYCLIN DOMAIN OF TFIIB (CHAIN M, RESIDUES 84-214) WERE FITTED AS POLY-ALANINE ...THE B-LINKER AND B-CYCLIN DOMAIN OF TFIIB (CHAIN M, RESIDUES 84-214) WERE FITTED AS POLY-ALANINE USING UNK RESIDUE NAMES DUE TO EXPERIMENTAL UNCERTAINTY IN THE ELECTRON DENSITY MAPS ABOUT THE EXACT SEQUENCE ASSIGNMENT RELATIVE TO THE S. CEREVISIAE AMINO ACID SEQUENCE. RESIDUES 215-345 WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THE COMPLETE CRYSTALLIZED SEQUENCE FOR THE CHAIN M IS AS FOLLOWS: MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRS EWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKK DNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRA EVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCS HLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVT EGTIKSGYKILYEHRDKLVDPQLIANGVVSLDSLPGVEKK

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.82 Å3/Da / Density % sol: 78.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 800 mM sodium ammonium tartrate, 100 mM HEPES pH 7.5, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: silicon crystal monochromator
RadiationMonochromator: Silicon crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 4.3→40 Å / Num. all: 83919 / Num. obs: 83919 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.13 / Net I/σ(I): 11.5
Reflection shellResolution: 4.3→4.3 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 6050 / Rsym value: 0.99 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.7.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: First 12-subunit RNA Polymerase II from PDB entry 3HOU

3hou


Resolution: 4.3→39.69 Å
Isotropic thermal model: Overall anisotropic temperature factor, one TLS group for all atoms, one group isotropic temperature factor for each residue
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: REFINEMENT WAS DONE AGAINST THE STRUCTURE FACTORS WITH FRIEDEL PAIRS MERGED AND A SHARPENING B-FACTOR OF -80 A**2 APPLIED. THE STRUCTURE WAS REFINED WITH ONE TLS GROUP FOR ALL ATOMS AND ...Details: REFINEMENT WAS DONE AGAINST THE STRUCTURE FACTORS WITH FRIEDEL PAIRS MERGED AND A SHARPENING B-FACTOR OF -80 A**2 APPLIED. THE STRUCTURE WAS REFINED WITH ONE TLS GROUP FOR ALL ATOMS AND ISOTROPIC GROUP B-FACTORS FOR WHOLE RESIDUES. ADDITIONAL DISTANCE RESTRAINTS WERE APPLIED TO STABILIZE THE ZINC COORDINATION SPHERE AND SECONDARY STRUCTURAL ELEMENTS. THE BUSTER ELECTRON DENSITY MAP COEFFICIENTS ARE AVAILABLE UPON REQUEST FROM DIRK KOSTREWA.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2058 2.45 %RANDOM
Rwork0.22 ---
all0.221 83918 --
obs0.221 83918 99.4 %-
Displacement parametersBiso mean: 124.4 Å2
Baniso -1Baniso -2Baniso -3
1-16.7149 Å20 Å20 Å2
2--25.3097 Å20 Å2
3----42.0246 Å2
Refine analyzeLuzzati coordinate error obs: 1.13 Å
Refinement stepCycle: LAST / Resolution: 4.3→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32323 0 9 0 32332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_angle_deg1.16
LS refinement shellResolution: 4.3→4.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 136 2.25 %
Rwork0.251 5908 -
obs-5908 99.4 %
Refinement TLS params.Method: refined / Origin x: 97.8862 Å / Origin y: 54.753 Å / Origin z: -2.3668 Å
111213212223313233
T0.1762 Å2-0.0337 Å20.1422 Å2--0.2862 Å20.0175 Å2--0.04 Å2
L0.7876 °2-0.0127 °2-0.0916 °2-0.8986 °2-0.0346 °2--0.7701 °2
S0.061 Å °0.0042 Å °0.2847 Å °0.3383 Å °-0.1643 Å °0.1776 Å °-0.0591 Å °-0.0789 Å °0.1033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }A2 - 1455
2X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }A3006 - 3008
3X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }C3 - 268
4X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }C3002
5X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }B20 - 1224
6X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }B3007
7X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }E2 - 215
8X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }D3 - 221
9X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }G1 - 171
10X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }F69 - 155
11X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }I2 - 120
12X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }I3003 - 3004
13X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }H2 - 146
14X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }K1 - 114
15X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }J1 - 65
16X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }J3001
17X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }M13 - 214
18X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }M3009
19X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }L25 - 70
20X-RAY DIFFRACTION1{ A|2 - A|1455 A|3006 - A|3008 C|3 - C|268 C|3002 - C|3002 B|20 - B|1224 B|3007 - B|3007 E|2 - E|215 D|3 - D|221 G|1 - G|171 F|69 - F|155 I|2 - I|120 I|3003 - I|3004 H|2 - H|146 K|1 - K|114 J|1 - J|65 J|3001 - J|3001 M|13 - M|214 M|3009 - M|3009 L|25 - L|70 L|3005 - L|3005 }L3005

+
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