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- PDB-3nfi: Crystal structure of tandem winged helix domain of RNA polymerase... -

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Basic information

Entry
Database: PDB / ID: 3nfi
TitleCrystal structure of tandem winged helix domain of RNA polymerase I subunit A49
ComponentsDNA-directed RNA polymerase I subunit RPA49
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION / winged helix / RNA polymerase / DNA binding
Function / homology
Function and homology information


RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / transcription by RNA polymerase I ...RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / transcription by RNA polymerase I / DNA-directed RNA polymerase activity / ribosome biogenesis / nucleolus / DNA binding / nucleus
Similarity search - Function
RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor
Similarity search - Domain/homology
DNA-directed RNA polymerase I subunit RPA49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsGeiger, S.R. / Lorenzen, K. / Schreieck, A. / Hanecker, P. / Kostrewa, D. / Heck, A.J.R. / Cramer, P.
CitationJournal: Mol.Cell / Year: 2010
Title: RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex.
Authors: Geiger, S.R. / Lorenzen, K. / Schreieck, A. / Hanecker, P. / Kostrewa, D. / Heck, A.J. / Cramer, P.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 25, 2015Group: Atomic model / Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit RPA49
B: DNA-directed RNA polymerase I subunit RPA49
C: DNA-directed RNA polymerase I subunit RPA49
D: DNA-directed RNA polymerase I subunit RPA49
E: DNA-directed RNA polymerase I subunit RPA49
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0636
Polymers135,7095
Non-polymers3541
Water14,160786
1
A: DNA-directed RNA polymerase I subunit RPA49


Theoretical massNumber of molelcules
Total (without water)27,1421
Polymers27,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-directed RNA polymerase I subunit RPA49


Theoretical massNumber of molelcules
Total (without water)27,1421
Polymers27,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA-directed RNA polymerase I subunit RPA49


Theoretical massNumber of molelcules
Total (without water)27,1421
Polymers27,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA-directed RNA polymerase I subunit RPA49


Theoretical massNumber of molelcules
Total (without water)27,1421
Polymers27,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DNA-directed RNA polymerase I subunit RPA49
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4962
Polymers27,1421
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.110, 78.100, 100.670
Angle α, β, γ (deg.)90.00, 113.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA-directed RNA polymerase I subunit RPA49 / A49 / DNA-directed RNA polymerase I 49 kDa polypeptide


Mass: 27141.715 Da / Num. of mol.: 5 / Fragment: UNP residues 171-403 / Mutation: L178M, L261M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: N0880, RPA49, RRN13, YNL248C / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 (DE) RIL / References: UniProt: Q01080, DNA-directed RNA polymerase
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPE4 E 1 IS PEG 4000 fragment

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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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG 3350, 50 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9790, 0.9790, 0.9180
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2009 / Details: torodial focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9181
ReflectionResolution: 1.9→80 Å / Num. all: 95580 / Num. obs: 94313 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 31.04 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.78
Reflection shellResolution: 1.9→2.08 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.606 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.9.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→27.82 Å / Cor.coef. Fo:Fc: 0.9527 / Cor.coef. Fo:Fc free: 0.9345 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 4711 5 %RANDOM
Rwork0.1886 ---
obs0.1903 94199 --
all-94199 --
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.0977 Å20 Å2-2.3971 Å2
2---0.0066 Å20 Å2
3----1.0911 Å2
Refine analyzeLuzzati coordinate error obs: 0.262 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8717 0 12 786 9515
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019109HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0412379HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3334SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1301HARMONIC5
X-RAY DIFFRACTIONt_it9109HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion15.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2554 309 4.84 %
Rwork0.2444 6079 -
all0.2449 6388 -
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)
10.36520.02530.04980.7259-0.36181.1862-0.02650.00160.01730.02880.03370.0147-0.0323-0.1177-0.0072-0.01780.0039-0.0331-0.0227-0.0031-0.05831.120614.462242.8828
24.3712-0.79241.29450.5255-0.06791.24880.03340.1043-0.2632-0.03150.00480.07720.0593-0.0564-0.0382-0.05340.0023-0.0487-0.13880.0223-0.124558.7738-0.372162.6149
32.3741-0.55910.7840.9493-0.16571.59710.1329-0.1008-0.24720.07860.02990.06110.0505-0.1383-0.1628-0.1114-0.0473-0.0352-0.08060.026-0.041135.187243.181377.5871
41.08680.20270.12071.3205-0.19290.9810.01080.0034-0.09310.0761-0.03420.0158-0.015-0.0370.0233-0.05360.0191-0.0107-0.0536-0.0029-0.065570.337349.010281.7861
51.16620.31890.37361.06460.09531.3009-0.10820.06520.1013-0.10990.02530.0432-0.22980.06740.0829-0.0035-0.0255-0.0489-0.07990.0181-0.083888.027416.646373.852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|*}A185 - 403
2X-RAY DIFFRACTION2{B|*}B172 - 403
3X-RAY DIFFRACTION3{C|*}C184 - 403
4X-RAY DIFFRACTION4{D|*}D184 - 403
5X-RAY DIFFRACTION5{E|*}E184 - 403

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