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- PDB-3h0g: RNA Polymerase II from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 3h0g
TitleRNA Polymerase II from Schizosaccharomyces pombe
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
KeywordsTRANSCRIPTION / Multi-protein complex / Polymerase / DNA-binding / DNA-directed RNA polymerase / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Zinc-finger
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / RNA polymerase II, holoenzyme / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / 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 III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter ...RNA Polymerase I Transcription Initiation / RNA polymerase II, holoenzyme / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / 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 III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / RNA Polymerase I Promoter Escape / mRNA Splicing - Major Pathway / Transcriptional regulation by small RNAs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / DNA-templated transcription elongation / intracellular phosphate ion homeostasis / chromatin-protein adaptor activity / termination of RNA polymerase II transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / 7-methylguanosine mRNA capping / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / pericentric heterochromatin / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / translation initiation factor binding / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / chromatin / nucleolus / mitochondrion / DNA binding / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L ...RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / N-terminal domain of TfIIb - #10 / Barwin-like endoglucanases - #20 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / Growth Hormone; Chain: A; / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / 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 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Homeodomain-like / Zinc finger TFIIS-type signature. / HRDC-like superfamily / 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 / 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. / DNA directed RNA polymerase, 7 kDa subunit / 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, 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit rpb7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit rpb4 / DNA-directed RNA polymerase II subunit rpb1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB2 ...DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit rpb7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit rpb4 / DNA-directed RNA polymerase II subunit rpb1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.65 Å
AuthorsSpahr, H. / Calero, G. / Bushnell, D.A. / Kornberg, R.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
Authors: Spahr, H. / Calero, G. / Bushnell, D.A. / Kornberg, R.D.
History
DepositionApr 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 10, 2015Group: Derived calculations
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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: DNA-directed RNA polymerase II subunit rpb1
N: DNA-directed RNA polymerase II subunit RPB2
O: DNA-directed RNA polymerase II subunit RPB3
P: DNA-directed RNA polymerase II subunit rpb4
Q: DNA-directed RNA polymerases I, II, and III subunit RPABC1
R: DNA-directed RNA polymerases I, II, and III subunit RPABC2
S: DNA-directed RNA polymerase II subunit rpb7
T: DNA-directed RNA polymerases I, II, and III subunit RPABC3
U: DNA-directed RNA polymerase II subunit RPB9
V: DNA-directed RNA polymerases I, II, and III subunit RPABC5
W: DNA-directed RNA polymerase II subunit RPB11
X: DNA-directed RNA polymerases I, II, and III subunit RPABC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)996,10342
Polymers995,00824
Non-polymers1,09518
Water00
1
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,05121
Polymers497,50412
Non-polymers5489
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area63020 Å2
ΔGint-460 kcal/mol
Surface area180240 Å2
MethodPISA
2
M: DNA-directed RNA polymerase II subunit rpb1
N: DNA-directed RNA polymerase II subunit RPB2
O: DNA-directed RNA polymerase II subunit RPB3
P: DNA-directed RNA polymerase II subunit rpb4
Q: DNA-directed RNA polymerases I, II, and III subunit RPABC1
R: DNA-directed RNA polymerases I, II, and III subunit RPABC2
S: DNA-directed RNA polymerase II subunit rpb7
T: DNA-directed RNA polymerases I, II, and III subunit RPABC3
U: DNA-directed RNA polymerase II subunit RPB9
V: DNA-directed RNA polymerases I, II, and III subunit RPABC5
W: DNA-directed RNA polymerase II subunit RPB11
X: DNA-directed RNA polymerases I, II, and III subunit RPABC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,05121
Polymers497,50412
Non-polymers5489
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62490 Å2
ΔGint-420 kcal/mol
Surface area178140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.034, 202.684, 391.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21M
12B
22N
13C
23O
14E
24Q
15G
25S
16D
26P
17H
27T
18K
28W
19F
29R

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYTHRTHRchain A and (resseq 3:127 or resseq 132:151 or resseq...AA3 - 1273 - 127
121ASPASPASPASPchain A and (resseq 3:127 or resseq 132:151 or resseq...AA132 - 151132 - 151
131GLYGLYTRPTRPchain A and (resseq 3:127 or resseq 132:151 or resseq...AA174 - 193174 - 193
141GLUGLUSERSERchain A and (resseq 3:127 or resseq 132:151 or resseq...AA212 - 257212 - 257
151SERSERTHRTHRchain A and (resseq 3:127 or resseq 132:151 or resseq...AA262 - 1086262 - 1086
161SERSERVALVALchain A and (resseq 3:127 or resseq 132:151 or resseq...AA1093 - 11491093 - 1149
171PHEPHETYRTYRchain A and (resseq 3:127 or resseq 132:151 or resseq...AA1265 - 14591265 - 1459
211GLYGLYTHRTHRchain M and (resseq 3:127 or resseq 132:151 or resseq...MM3 - 1273 - 127
221ASPASPASPASPchain M and (resseq 3:127 or resseq 132:151 or resseq...MM132 - 151132 - 151
231GLYGLYTRPTRPchain M and (resseq 3:127 or resseq 132:151 or resseq...MM174 - 193174 - 193
241GLUGLUSERSERchain M and (resseq 3:127 or resseq 132:151 or resseq...MM212 - 257212 - 257
251SERSERTHRTHRchain M and (resseq 3:127 or resseq 132:151 or resseq...MM262 - 1086262 - 1086
261SERSERVALVALchain M and (resseq 3:127 or resseq 132:151 or resseq...MM1093 - 11491093 - 1149
271PHEPHETYRTYRchain M and (resseq 3:127 or resseq 132:151 or resseq...MM1265 - 14591265 - 1459
112GLUGLUTHRTHRchain B and (resseq 10:57 or resseq 77:121 or resseq...BB10 - 5710 - 57
122ILEILELYSLYSchain B and (resseq 10:57 or resseq 77:121 or resseq...BB77 - 12177 - 121
132LYSLYSGLYGLYchain B and (resseq 10:57 or resseq 77:121 or resseq...BB149 - 324149 - 324
142GLUGLUGLYGLYchain B and (resseq 10:57 or resseq 77:121 or resseq...BB332 - 489332 - 489
152ALAALAALAALAchain B and (resseq 10:57 or resseq 77:121 or resseq...BB495 - 905495 - 905
162LYSLYSHISHISchain B and (resseq 10:57 or resseq 77:121 or resseq...BB923 - 1209923 - 1209
212GLUGLUTHRTHRchain N and (resseq 10:57 or resseq 77:121 or resseq...NN10 - 5710 - 57
222ILEILELYSLYSchain N and (resseq 10:57 or resseq 77:121 or resseq...NN77 - 12177 - 121
232LYSLYSGLYGLYchain N and (resseq 10:57 or resseq 77:121 or resseq...NN149 - 324149 - 324
242GLUGLUGLYGLYchain N and (resseq 10:57 or resseq 77:121 or resseq...NN332 - 489332 - 489
252ALAALAALAALAchain N and (resseq 10:57 or resseq 77:121 or resseq...NN495 - 905495 - 905
262LYSLYSHISHISchain N and (resseq 10:57 or resseq 77:121 or resseq...NN923 - 1209923 - 1209
113GLUGLUGLUGLUchain C and (resseq 4:266 )CC4 - 2664 - 266
213GLUGLUGLUGLUchain O and (resseq 4:266 )OO4 - 2664 - 266
114GLUGLUALAALAchain E and (resseq 4:210 )EE4 - 2104 - 210
214GLUGLUALAALAchain Q and (resseq 4:210 )QQ4 - 2104 - 210
115PHEPHESERSERchain G and (resseq 4:40 or resseq 44:172 )GG4 - 404 - 40
125GLYGLYLEULEUchain G and (resseq 4:40 or resseq 44:172 )GG44 - 17244 - 172
215PHEPHESERSERchain S and (resseq 4:40 or resseq 44:172 )SS4 - 404 - 40
225GLYGLYLEULEUchain S and (resseq 4:40 or resseq 44:172 )SS44 - 17244 - 172
116PHEPHEGLNGLNchain D and (resseq 6:134 )DD6 - 1346 - 134
216PHEPHEGLNGLNchain P and (resseq 6:134 )PP6 - 1346 - 134
117SERSERARGARGchain H and (resseq 2:125 )HH2 - 1252 - 125
217SERSERARGARGchain T and (resseq 2:125 )TT2 - 1252 - 125
118METMETMETMETchain K and (resseq 1:112 )KK1 - 1121 - 112
218METMETMETMETchain W and (resseq 1:112 )WW1 - 1121 - 112
119VALVALILEILEchain F and (resseq 64:142 )FF64 - 14264 - 142
219VALVALILEILEchain R and (resseq 64:142 )RR64 - 14264 - 142

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

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 14 molecules AMBNCODPGSIUKW

#1: Protein DNA-directed RNA polymerase II subunit rpb1 / RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III largest subunit


Mass: 194372.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: P36594, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit B2 / RNA polymerase II subunit 2 / DNA-directed RNA polymerase II 138 kDa ...RNA polymerase II subunit B2 / RNA polymerase II subunit 2 / DNA-directed RNA polymerase II 138 kDa polypeptide


Mass: 138027.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: Q02061, 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 33 kDa polypeptide


Mass: 33748.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: P37382
#4: Protein DNA-directed RNA polymerase II subunit rpb4 / RNA polymerase II subunit B4


Mass: 15379.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: O74825
#7: Protein DNA-directed RNA polymerase II subunit rpb7 / RNA polymerase II subunit B7


Mass: 19121.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: O14459
#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 13.2 kDa polypeptide


Mass: 13192.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: O74635
#11: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 14.1 kDa polypeptide


Mass: 14143.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: P87123

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 10 molecules EQFRHTJVLX

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / RPC24B


Mass: 23954.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: Q09191
#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 15 ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 15 kDa polypeptide / RPC16


Mass: 15742.497 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: P36595
#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 / RPC14


Mass: 14317.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: Q92399
#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 / RPC8


Mass: 8286.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: O13877
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7216.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / Strain: 972h- / References: UniProt: P48011

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Non-polymers , 2 types, 18 molecules

#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#14: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 50mM MES pH 6.3, 300mM ammonium acetate, 5-6.5% (w/v) PEG 4000, 10mM DTT, 7.1mM C8E5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 138872 / % possible obs: 96.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.702
Reflection shellResolution: 3.65→3.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.3 / Num. measured all: 45357 / Num. unique all: 19808 / Rsym value: 0.6 / % possible all: 95.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WCM

1wcm


Resolution: 3.65→48.695 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.73 / σ(F): 0.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.321 3725 1.44 %RANDOM
Rwork0.297 ---
obs0.297 138803 92.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.89 Å2 / ksol: 0.246 e/Å3
Displacement parametersBiso max: 676.43 Å2 / Biso mean: 203.114 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-40.084 Å2-0 Å20 Å2
2---72.284 Å2-0 Å2
3---32.2 Å2
Refinement stepCycle: LAST / Resolution: 3.65→48.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62852 0 18 0 62870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864027
X-RAY DIFFRACTIONf_angle_d1.11786539
X-RAY DIFFRACTIONf_chiral_restr0.0679676
X-RAY DIFFRACTIONf_plane_restr0.01111264
X-RAY DIFFRACTIONf_dihedral_angle_d17.25624123
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A10171X-RAY DIFFRACTIONPOSITIONAL0.527
12M10171X-RAY DIFFRACTIONPOSITIONAL0.527
21B8982X-RAY DIFFRACTIONPOSITIONAL0.272
22N8982X-RAY DIFFRACTIONPOSITIONAL0.272
31C2088X-RAY DIFFRACTIONPOSITIONAL0.053
32O2088X-RAY DIFFRACTIONPOSITIONAL0.053
41E1663X-RAY DIFFRACTIONPOSITIONAL0.001
42Q1663X-RAY DIFFRACTIONPOSITIONAL0.001
51G1294X-RAY DIFFRACTIONPOSITIONAL0.002
52S1294X-RAY DIFFRACTIONPOSITIONAL0.002
61D1028X-RAY DIFFRACTIONPOSITIONAL0.181
62P1028X-RAY DIFFRACTIONPOSITIONAL0.181
71H996X-RAY DIFFRACTIONPOSITIONAL0.001
72T996X-RAY DIFFRACTIONPOSITIONAL0.001
81K904X-RAY DIFFRACTIONPOSITIONAL0.08
82W904X-RAY DIFFRACTIONPOSITIONAL0.08
91F632X-RAY DIFFRACTIONPOSITIONAL0.06
92R632X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.65-3.6960.4891290.4279048917788
3.696-3.7450.3731270.3948976910389
3.745-3.7960.3521370.3749134927190
3.796-3.850.4191360.3749069920590
3.85-3.9080.431300.3959148927890
3.908-3.9690.3841350.379213934890
3.969-4.0340.3471300.3489173930391
4.034-4.1030.3151360.3279162929891
4.103-4.1780.311380.3249304944291
4.178-4.2580.3161390.329271941092
4.258-4.3450.3261370.3049361949892
4.345-4.4390.3211350.2989328946392
4.439-4.5430.2751340.2839480961493
4.543-4.6560.3341440.2759573971794
4.656-4.7820.3091450.2769642978795
4.782-4.9230.311440.2689747989196
4.923-5.0810.2861440.2769773991796
5.081-5.2630.3111410.2799726986796
5.263-5.4730.2951450.2819733987896
5.473-5.7220.2831410.2869702984396
5.722-6.0230.3311420.2959748989095
6.023-6.40.3131450.3079610975595
6.4-6.8920.3941410.2979578971995
6.892-7.5840.291370.279580971794
7.584-8.6760.2621380.2179561969994
8.676-10.910.1851430.1869547969094
10.91-48.6990.3191320.2869309944192
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)
10.92330.4720.21290.1399-0.01960.1873-0.24720.17050.1437-0.10390.18110.08420.1498-0.15260.04840.4034-0.0730.07191.71980.01870.4142-13.5843-38.7933-31.5382
20.8527-0.6359-1.39621.01290.3226-0.67960.43330.0736-0.4682-0.0171-0.15620.4205-0.25040.4249-0.33540.9397-0.4509-0.04271.6373-0.31081.0662-6.2392-94.1707-50.534
30.4665-0.0531-0.06331.0630.06320.5293-0.08270.0582-0.052-0.1449-0.0402-0.24210.040.11570.11290.52490.00690.01681.6499-0.00410.571738.4178-51.8605-27.969
40.7013-0.4715-1.55050.25251.5779-0.21030.27140.65390.05170.1319-0.18690.0612-0.2625-0.0146-0.09111.0323-0.0793-0.24491.7790.65310.5391.23536.3716-86.7052
50.96630.0831-0.10860.4320.8631-1.3545-0.48580.1478-0.0943-0.11990.29610.1622-0.4223-0.02170.14981.112-0.2821-0.02191.83480.08390.23256.157-40.8214-78.025
60.0682-0.01080.39670.64790.25930.30920.14540.0133-0.0529-0.12-0.1837-0.194-0.4913-0.03050.0331.54110.05040.36841.5222-0.04691.359545.761454.4286-61.5616
71.6401-0.74370.6940.4538-0.1228-1.053-0.0701-0.1260.02350.1310.6117-0.1803-0.0378-0.0636-0.60981.8433-0.70030.3231.5106-0.02091.008299.735977.3317-58.9729
80.4580.4390.27540.23230.26780.32580.08490.1592-0.409-0.12370.1035-0.22670.0370.3224-0.19521.20590.09130.19031.8659-0.26361.372581.648615.1664-70.1004
90.99370.16750.89620.99810.4087-1.2514-1.0034-0.67670.32130.46940.74790.13780.12131.04140.22421.73250.3720.50071.9444-0.04560.945729.485125.47413.0744
101.8626-0.84210.056-0.30010.03820.2453-0.3378-0.6561.31120.18330.3957-0.5470.3059-0.035-0.16950.83560.2441-0.40351.781-0.55311.662768.009543.4078-17.923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(((chain A and resid 809:1141) or (chain A and resid 1275:1394) or (chain E) or (chain F)))A809 - 1141
2X-RAY DIFFRACTION1(((chain A and resid 809:1141) or (chain A and resid 1275:1394) or (chain E) or (chain F)))A1275 - 1394
3X-RAY DIFFRACTION1(((chain A and resid 809:1141) or (chain A and resid 1275:1394) or (chain E) or (chain F)))E0
4X-RAY DIFFRACTION1(((chain A and resid 809:1141) or (chain A and resid 1275:1394) or (chain E) or (chain F)))F0
5X-RAY DIFFRACTION2(((chain A and resid 1142:1274) or (chain B and resid 218:405) or (chain I and resid 1:39)))A1142 - 1274
6X-RAY DIFFRACTION2(((chain A and resid 1142:1274) or (chain B and resid 218:405) or (chain I and resid 1:39)))B218 - 405
7X-RAY DIFFRACTION2(((chain A and resid 1142:1274) or (chain B and resid 218:405) or (chain I and resid 1:39)))I1 - 39
8X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))A347 - 808
9X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))B1 - 217
10X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))B406 - 1150
11X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))C0
12X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))J0
13X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))K0
14X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))L0
15X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))H0
16X-RAY DIFFRACTION3(((chain A and resid 347:808) or (chain B and (resid 1:217 or resid 406:1150)) or chain C or chain J or chain K or chain L or chain H or (chain I and resid 40:122)))I40 - 122
17X-RAY DIFFRACTION4((chain G) or (chain D))G0
18X-RAY DIFFRACTION5(((chain A and resid 1:346) or (chain A and resid 1395:1445) or (chain B and resid 1151:1224)))A1 - 346
19X-RAY DIFFRACTION5(((chain A and resid 1:346) or (chain A and resid 1395:1445) or (chain B and resid 1151:1224)))A1395 - 1445
20X-RAY DIFFRACTION5(((chain A and resid 1:346) or (chain A and resid 1395:1445) or (chain B and resid 1151:1224)))B1151 - 1224
21X-RAY DIFFRACTION6(((chain M and resid 809:1141) or (chain M and resid 1275:1394) or (chain Q) or (chain R)))M809 - 1141
22X-RAY DIFFRACTION6(((chain M and resid 809:1141) or (chain M and resid 1275:1394) or (chain Q) or (chain R)))M1275 - 1394
23X-RAY DIFFRACTION6(((chain M and resid 809:1141) or (chain M and resid 1275:1394) or (chain Q) or (chain R)))Q0
24X-RAY DIFFRACTION6(((chain M and resid 809:1141) or (chain M and resid 1275:1394) or (chain Q) or (chain R)))R0
25X-RAY DIFFRACTION7(((chain M and resid 1142:1274) or (chain N and resid 218:405) or (chain U and resid 1:39)))M1142 - 1274
26X-RAY DIFFRACTION7(((chain M and resid 1142:1274) or (chain N and resid 218:405) or (chain U and resid 1:39)))N218 - 405
27X-RAY DIFFRACTION7(((chain M and resid 1142:1274) or (chain N and resid 218:405) or (chain U and resid 1:39)))U1 - 39
28X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))M347 - 808
29X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))N1 - 217
30X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))N406 - 1150
31X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))O0
32X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))V0
33X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))W0
34X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))X0
35X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))T0
36X-RAY DIFFRACTION8(((chain M and resid 347:808) or (chain N and (resid 1:217 or resid 406:1150)) or chain O or chain V or chain W or chain X or chain T or (chain U and resid 40:122)))U40 - 122
37X-RAY DIFFRACTION9((chain S) or (chain P))S0
38X-RAY DIFFRACTION10(((chain M and resid 1:346) or (chain M and resid 1395:1445) or (chain N and resid 1151:1224)))M1 - 346
39X-RAY DIFFRACTION10(((chain M and resid 1:346) or (chain M and resid 1395:1445) or (chain N and resid 1151:1224)))M1395 - 1445
40X-RAY DIFFRACTION10(((chain M and resid 1:346) or (chain M and resid 1395:1445) or (chain N and resid 1151:1224)))N1151 - 1224

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