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- PDB-4c2m: Structure of RNA polymerase I at 2.8 A resolution -

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Entry
Database: PDB / ID: 4c2m
TitleStructure of RNA polymerase I at 2.8 A resolution
Components
  • (DNA-DIRECTED RNA POLYMERASE I SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ...) x 2
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
KeywordsTRANSCRIPTION / RIBOSOME BIOGENESIS
Function / homologyRPA43 OB domain in RNA Pol I / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit ...RPA43 OB domain in RNA Pol I / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb6 / RNA polymerase Rpb5, C-terminal domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb2, domain 3 / RPB6/omega subunit-like superfamily / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / mRNA Splicing - Minor Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase II transcribes snRNA genes / mRNA Capping / RNA Polymerase I Transcription Initiation / Formation of the Early Elongation Complex / 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 Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / Zinc finger TFIIS-type profile. / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / A49-like RNA polymerase I associated factor / RNA polymerase I, Rpa2 specific domain / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases beta chain signature. / Zinc finger TFIIS-type signature. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases, subunit N, zinc binding site / Pol I subunit A12, C-terminal zinc ribbon / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase Rpb7, N-terminal / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb2, domain 7 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA pol I, largest subunit / RNA polymerase, beta subunit, protrusion / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus
Function and homology information
Specimen sourceSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.8 Å resolution
AuthorsEngel, C. / Sainsbury, S. / Cheung, A.C. / Kostrewa, D. / Cramer, P.
CitationJournal: Nature / Year: 2013
Title: RNA Polymerase I Structure and Transcription Regulation.
Authors: Engel, C. / Sainsbury, S. / Cheung, A.C. / Kostrewa, D. / Cramer, P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 19, 2013 / Release: Oct 23, 2013
RevisionDateData content typeGroupProviderType
1.0Oct 23, 2013Structure modelrepositoryInitial release
1.1Nov 6, 2013Structure modelDatabase references
1.2Aug 19, 2015Structure modelDerived calculations
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2B" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "2B" 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 "AF" 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 "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "PF" 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 "PI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "VC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
2: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
3: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
4: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
A: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
B: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
C: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
D: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
N: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
O: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
P: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
Q: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
R: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
S: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
T: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
U: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
V: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
W: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
X: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
Y: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
Z: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,254,19546
Polyers1,253,08730
Non-polymers1,10816
Water4,720262
1
A: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
B: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
C: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
D: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
N: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
O: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)627,09723
Polyers626,54315
Non-polymers5548
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)99110
ΔGint (kcal/M)-545.1
Surface area (Å2)204050
MethodPQS
2
1: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
2: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
3: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
4: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
P: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
Q: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
R: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
S: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
T: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
U: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
V: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
W: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
X: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
Y: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
Z: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)627,09723
Polyers626,54315
Non-polymers5548
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)98310
ΔGint (kcal/M)-543.3
Surface area (Å2)203550
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)122.740, 139.020, 209.550
Angle α, β, γ (deg.)108.06, 95.40, 93.85
Int Tables number1
Space group name H-MP 1

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Components

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 10 molecules 1LETFUHWJY

#1: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA polymerase / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC4 / ABC10-ALPHA / RPB12


Mass: 7729.969 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P40422
#9: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 27 KDA POLYPEPTIDE / RPB5


Mass: 25117.094 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P20434
#10: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA polymerase / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 23 KDA POLYPEPTIDE / RPB6


Mass: 17931.834 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P20435
#11: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / RNA polymerase / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 14.5 KDA POLYPEPTIDE / RPB8


Mass: 16525.363 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P20436
#13: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA polymerase / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 8.3 KDA POLYPEPTIDE / RPB10


Mass: 8290.732 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P22139

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DNA-DIRECTED RNA POLYMERASE I SUBUNIT ... , 7 types, 16 molecules 2M3N4GOVAPBQDSIX

#2: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49 / Polymerase / A49 / DNA-DIRECTED RNA POLYMERASE I 49 KDA POLYPEPTIDE


Mass: 46721.707 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: Q01080
#3: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34 / Polymerase / A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POLYPEPTIDE / A34.5 / A34.5


Mass: 26933.518 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P47006
#4: Protein/peptide
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43 / Polymerase / A43 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 36 KDA POLYPEPTIDE / A43


Mass: 36264.852 Da / Num. of mol.: 4 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P46669
#5: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190 / Polymerase / A190 / DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT


Mass: 186676.969 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P10964, DNA-directed RNA polymerase
#6: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135 / Polymerase / DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DNA-DIRECTED RNA POLYMERASE I POLYPEPTIDE 2 / RNA POLYMERASE I SUBUNIT 2 / A135


Mass: 135910.328 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P22138, DNA-directed RNA polymerase
#8: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14 / Polymerase / A14 / DNA-DIRECTED RNA POLYMERASE I 14 KDA POLYPEPTIDE / A14


Mass: 14599.128 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P50106
#12: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12 / Polymerase / A12 / A12.2 / DNA-DIRECTED RNA POLYMERASE I 13.7 KDA POLYPEPTIDE / A12.2


Mass: 13676.566 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P32529

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DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ... , 2 types, 4 molecules CRKZ

#7: Protein/peptide DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 / RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RN A POLYMERASES I AND III 40 KDA POLYPEPTIDE / AC40 / C40 / AC40


Mass: 37732.613 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P07703
#14: Protein/peptide DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2 / RNA POLYMERASES I AND III SUBUNIT AC2 / DNA-DIRECTED R NA POLYMERASES I AND III 16 KDA POLYPEPTIDE / RPA19 / AC19


Mass: 16167.860 Da / Num. of mol.: 2 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P28000

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Non-polymers , 3 types, 278 molecules

#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Formula: Zn / Zinc
#16: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Formula: SO4 / Sulfate
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.85 / Density percent sol: 56.9 % / Description: NONE
Crystal growpH: 7
Details: 10% PEG4000, 300MM AMMONIUM ACETATE, 50MM HEPES PH 7.5, 5MM TCEP

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Data collection

Diffraction
IDMean temperatureCrystal ID
11001
21001
Source
SourceTypeSynchrotron siteBeamlineIdWavelength
SYNCHROTRONSLS BEAMLINE X10SASLSX10SA11.0
SYNCHROTRONSLS BEAMLINE X06SASLSX06SA21.28288
Detector
TypeIdDetector
DECTRIS PILATUS 6M1PIXEL
DECTRIS PILATUS 6M2PIXEL
Radiation
IdDiffraction protocolMonochromatic or laue m lScattering typeWavelength ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelengthRelative weight
11.01.0
21.282881.0
ReflectionD resolution high: 2.8 Å / D resolution low: 4 Å / Number obs: 320814 / Observed criterion sigma I: 1.5 / Rmerge I obs: 0.24 / NetI over sigmaI: 9.61 / Redundancy: 13.1 % / Percent possible obs: 99.9
Reflection shellHighest resolution: 2.8 Å / Lowest resolution: 2.87 Å / MeanI over sigI obs: 1.52 / Redundancy: 11.5 % / Percent possible all: 99.8

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
autoSHARPphasing
PARROTphasing
PHENIXrefinement
RefineMethod to determine structure: MAD
Starting model: NONE

Overall SU ML: 0.39 / Sigma F: 1.99 / Overall phase error: 23.43 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2099 / R factor R work: 0.1689 / R factor obs: 0.1697 / Highest resolution: 2.8 Å / Lowest resolution: 39.292 Å / Number reflection R free: 6493 / Number reflection obs: 320815 / Percent reflection R free: 2 / Percent reflection obs: 99.91
Refine hist #LASTHighest resolution: 2.8 Å / Lowest resolution: 39.292 Å
Number of atoms included #LASTProtein: 68821 / Nucleic acid: 0 / Ligand: 24 / Solvent: 262 / Total: 69107
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01070209
X-RAY DIFFRACTIONf_angle_d1.24194762
X-RAY DIFFRACTIONf_dihedral_angle_d16.31826576
X-RAY DIFFRACTIONf_chiral_restr0.08410577
X-RAY DIFFRACTIONf_plane_restr0.00512274
Refine LS restraints ncs

Refine ID: X-RAY DIFFRACTION / Type: POSITIONAL

Dom IDAuth asym IDEns IDNumberRms dev position
1A1625
2P16250.075
1A2475
2P24750.037
1A3783
2P37830.055
1A4427
2P44270.092
1A5141
2P51410.035
1A6489
2P64890.101
1A7279
2P72790.042
1A81367
2P813670.041
1A91368
2P913680.042
1A101220
2P1012200.042
1A11316
2P113160.054
1A121012
2P1210120.041
1A13341
2P133410.041
1A14921
2P149210.043
1A15290
2P152900.083
1A16524
2P165240.048
1B17544
2Q175440.038
1B18885
2Q188850.039
1B191632
2Q1916320.050
1B20677
2Q206770.092
1B211651
2Q2116510.068
1B22787
2Q227870.045
1B23865
2Q238650.030
1B241004
2Q2410040.055
1B251216
2Q2512160.047
1C26377
2R263770.145
1C271121
2R2711210.048
1C28915
2R289150.032
1D29459
2S294590.029
1G30890
2V308900.036
1G31618
2V316180.058
1O32404
24324040.033
1E331161
2T3311610.027
1E34565
2T345650.065
1F35823
2U358230.037
1H361052
2W3610520.032
1I37516
2X375160.043
1I38384
2X383840.032
1J39570
2Y395700.036
1K40786
2Z407860.055
1L41353
21413530.029
1M42814
22428140.031
1N43816
23438160.031
1N44320
23443200.032
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.80000.34850.31802.831821210451100.00
2.83180.33970.30002.865121810460100.00
2.86510.32250.28582.900023610483100.00
2.90000.30650.26542.936723610465100.00
2.93670.30110.25392.975421110453100.00
2.97540.31460.25493.016122310481100.00
3.01610.27030.24763.059223010455100.00
3.05920.31740.24693.104823610423100.00
3.10480.33040.24593.153320810561100.00
3.15330.28170.24313.205021010452100.00
3.20500.27060.22553.260224810466100.00
3.26020.29450.22043.319519810572100.00
3.31950.25870.21093.383320110465100.00
3.38330.24780.19943.452321710411100.00
3.45230.22600.18933.527422710479100.00
3.52740.23810.18583.609420610565100.00
3.60940.21900.16933.699519710428100.00
3.69950.21670.16273.799521510469100.00
3.79950.20620.15923.911220910507100.00
3.91120.21660.15264.037321710449100.00
4.03730.20150.14784.181521010538100.00
4.18150.17350.13364.348721510527100.00
4.34870.15910.12984.546320610456100.00
4.54630.16650.12554.785622010513100.00
4.78560.16880.12695.084922710452100.00
5.08490.15550.13385.476522310483100.00
5.47650.18500.14376.025920010500100.00
6.02590.19600.14916.893820410504100.00
6.89380.17110.13828.670022210477100.00
8.67000.15540.146439.29632111037799.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.8457-0.28590.10470.51880.02050.32640.01240.13860.3649-0.0644-0.0437-0.1187-0.14510.0404-0.00000.5303-0.04100.00240.48750.09650.630449.5617129.4574160.7670
20.7875-0.0413-0.05850.9547-0.28090.99060.0092-0.0915-0.12670.1126-0.03810.10660.1300-0.0708-0.00010.4925-0.03030.00120.53230.04950.486615.469989.3582163.8487
31.3251-0.0103-0.38741.22510.08521.1674-0.01620.0912-0.4279-0.0799-0.0770-0.23590.16470.1425-0.00020.52770.0290-0.01110.58720.03230.633640.157869.4737136.6994
41.1614-0.0249-0.00471.00420.40491.20390.05800.8883-0.3307-0.5104-0.22570.19510.2821-0.3358-0.01090.88910.0662-0.20871.3082-0.13500.68005.380681.6845107.1565
51.0481-0.24900.31121.06610.03450.7146-0.0843-0.50600.12750.56020.2702-0.61600.14310.31170.00020.89330.1725-0.30011.0172-0.14730.9531100.735994.2562206.2561
60.12550.02940.00450.08070.04470.0294-0.3526-0.5349-1.12980.25960.28520.31211.05090.1412-0.00171.08190.1868-0.07610.91050.19610.860085.549968.8476202.3236
70.06360.08330.04330.12520.10130.14870.09400.19020.3930-0.1858-0.00790.3877-0.3311-0.55210.00010.97290.08490.02430.84460.17910.746145.293293.4795201.7095
80.08120.11110.09190.18970.17420.1661-0.15260.1593-0.02100.1446-0.36820.48750.3899-0.79020.00060.8157-0.10070.05290.8673-0.08130.757930.7226111.5067182.3912
90.52110.47420.30500.76170.21010.6190-0.0249-0.0379-0.50200.00840.0499-0.19440.4030-0.15360.00010.88540.0083-0.05510.79630.17720.684455.734667.7819203.1779
100.8446-0.4506-0.20610.81370.18870.9853-0.1423-0.0734-0.09460.16020.0743-0.11460.20810.12790.00010.59220.0288-0.06650.57870.04040.557279.910385.4226183.0671
110.4143-0.05940.24160.46460.19610.2566-0.1556-0.11760.19120.20330.2497-0.26270.11280.18470.00010.52680.0372-0.15030.6563-0.04540.632182.6974106.7574193.8550
120.6955-0.1427-0.00110.76690.27390.68740.0244-0.31640.34120.1424-0.09640.3790-0.3050-0.3942-0.00020.74130.17140.08330.7904-0.15611.0088-3.0100140.1705183.9891
130.79550.05630.11030.72330.23390.6128-0.0490-0.11720.22400.0755-0.18510.4095-0.2239-0.1741-0.01140.75180.04590.03310.5950-0.12290.788440.5961125.924754.8951
140.7830-0.04730.00661.11740.59021.44260.00140.1705-0.12020.0727-0.0093-0.07130.15210.23840.00030.63660.00710.04330.63580.02510.472579.869390.325653.1921
151.3649-0.0962-0.30611.40600.08481.27280.0506-0.0261-0.41800.1393-0.13420.28910.2733-0.1420-0.00030.8831-0.07200.02740.5854-0.00290.635557.100167.258179.3932
160.7712-0.00770.23570.2940-0.70511.54060.0880-0.3952-0.18250.0414-0.1070-0.02070.30590.36310.00011.0382-0.0027-0.08780.97250.04000.572088.569385.1618111.0841
170.86790.37480.22711.03440.26150.6100-0.11130.3664-0.0835-0.4326-0.36120.9151-0.1769-0.5728-0.02620.83750.1021-0.23461.4629-0.65121.7693-4.163883.51528.1337
180.1241-0.11460.17010.1447-0.22260.34420.1456-0.1740-0.82690.0087-0.29110.58690.6624-0.05110.02220.8221-0.09760.05921.2175-0.68471.731713.652460.301813.3168
190.0667-0.0593-0.00070.1026-0.07110.10040.05780.03280.17410.2879-0.25020.1639-0.21000.12430.00110.7564-0.0470-0.09080.8881-0.32070.917948.112487.195414.4203
200.0859-0.03500.08720.1205-0.09280.1181-0.1485-0.1992-0.24310.0328-0.3464-0.29520.18710.69430.00101.09810.07110.03441.00960.04980.932062.0321109.828134.3912
210.6127-0.52380.39190.5793-0.28780.6648-0.0592-0.1298-0.60070.0070-0.11360.57620.38850.19470.00030.7200-0.00130.06200.9038-0.31231.087543.413362.787213.4834
220.4579-0.01040.05980.64830.03770.6098-0.0896-0.0377-0.33570.1852-0.25490.51630.2106-0.30540.00030.6041-0.09760.16270.8681-0.38611.296916.255577.795732.5526
230.1873-0.1143-0.06640.2175-0.15660.2894-0.22010.1501-0.0121-0.1077-0.12490.6020-0.0463-0.5024-0.02140.54310.1145-0.19790.9463-0.44441.302411.422698.388121.3402
240.67020.15410.12660.5970-0.25980.6047-0.03220.50910.5471-0.2255-0.0115-0.1849-0.55400.4894-0.00021.1027-0.30280.04030.90300.20320.783691.5535142.785232.9817
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 654:1013 OR RESID 1361:1367) OR CHAIN B AND (RESID 8:209 OR RESID 400:553 OR RESID 647:1068) OR CHAIN C OR CHAIN J OR CHAIN K OR CHAIN L OR CHAIN N AND RESID 147:180
2X-RAY DIFFRACTION2CHAIN A AND (RESID 477:653 OR RESID 1014:1261 OR RESID 1368:1395 OR RESID 1500:1608) OR CHAIN B AND RESID 1069:1092 OR CHAIN E OR CHAIN F AND RESID 73:154
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1:476 OR RESID 1609:1649 OR RESID 3001:3002) OR CHAIN B AND (RESID 1093-1203 OR RESID 3001) OR CHAIN O
4X-RAY DIFFRACTION4CHAIN A AND RESID 1650:1664 OR CHAIN D OR CHAIN F AND RESID 55:72 OR CHAIN G
5X-RAY DIFFRACTION5CHAIN M OR CHAIN N AND RESID 25:146
6X-RAY DIFFRACTION6CHAIN I AND (RESID 2:52 OR RESID 3001)
7X-RAY DIFFRACTION7CHAIN I AND RESID 53:78
8X-RAY DIFFRACTION8CHAIN I AND (RESID 79:125 OR RESID 3002)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 1262:1337 OR RESID 1440:1499)
10X-RAY DIFFRACTION10CHAIN B AND RESID 210:399
11X-RAY DIFFRACTION11CHAIN B AND RESID 554:646
12X-RAY DIFFRACTION12CHAIN H
13X-RAY DIFFRACTION13CHAIN P AND (RESID 654:1013 OR RESID 1361:1367) OR CHAIN Q AND (RESID 8:209 OR RESID 400:553 OR RESID 647:1068) OR CHAIN R OR CHAIN Y OR CHAIN Z OR CHAIN 1 OR CHAIN 3 AND RESID 147:181
14X-RAY DIFFRACTION14CHAIN P AND (RESID 477:653 OR RESID 1014:1261 OR RESID 1368:1395 OR RESID 1500:1608) OR CHAIN Q AND RESID 1069:1092 OR CHAIN T OR CHAIN U AND RESID 73:154
15X-RAY DIFFRACTION15CHAIN P AND (RESID 1:476 OR RESID 1609:1649 OR RESID 3001:3002) OR CHAIN Q AND (RESID 1093-1203 OR RESID 3001) OR CHAIN 4
16X-RAY DIFFRACTION16CHAIN P AND RESID 1650:1664 OR CHAIN S OR CHAIN U AND RESID 55:72 OR CHAIN V
17X-RAY DIFFRACTION17CHAIN 2 OR CHAIN 3 AND RESID 25:146
18X-RAY DIFFRACTION18CHAIN X AND (RESID 2:52 OR RESID 3001)
19X-RAY DIFFRACTION19CHAIN X AND RESID 53:78
20X-RAY DIFFRACTION20CHAIN X AND (RESID 79:125 OR RESID 3002)
21X-RAY DIFFRACTION21CHAIN P AND (RESID 1262:1337 OR RESID 1440:1499)
22X-RAY DIFFRACTION22CHAIN Q AND RESID 210:399
23X-RAY DIFFRACTION23CHAIN Q AND RESID 554:646
24X-RAY DIFFRACTION24CHAIN W

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