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- PDB-3u1u: Crystal structure of RNA polymerase-associated protein RTF1 homol... -

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Basic information

Entry
Database: PDB / ID: 3u1u
TitleCrystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain
ComponentsRNA polymerase-associated protein RTF1 homolog
KeywordsTRANSCRIPTION / PLUS-3 / transcription elongation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


blastocyst growth / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / stem cell population maintenance / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / Wnt signaling pathway ...blastocyst growth / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / endodermal cell fate commitment / stem cell population maintenance / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / single-stranded DNA binding / nucleolus / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm
Similarity search - Function
Plus-3 domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA polymerase-associated protein RTF1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsGuo, Y. / Tempel, W. / Bian, C. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain
Authors: Guo, Y. / Tempel, W. / Bian, C. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase-associated protein RTF1 homolog
B: RNA polymerase-associated protein RTF1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,31230
Polymers31,8352
Non-polymers47628
Water1,856103
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-59 kcal/mol
Surface area14060 Å2
MethodPISA
2
B: RNA polymerase-associated protein RTF1 homolog
hetero molecules

A: RNA polymerase-associated protein RTF1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,31230
Polymers31,8352
Non-polymers47628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area2270 Å2
ΔGint-60 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.479, 50.369, 69.776
Angle α, β, γ (deg.)90.00, 103.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA polymerase-associated protein RTF1 homolog


Mass: 15917.687 Da / Num. of mol.: 2 / Fragment: unp residues 347-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTF1, KIAA0252 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q92541
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 23 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 291 K / Method: sitting drop vapor diffusion / pH: 5.5
Details: 25% PEG-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 5.5, sitting drop vapor diffusion, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
xds1001
11
Diffraction sourceSource: ROTATING ANODE / Type: Rigaku FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 29993 / Num. obs: 29882 / % possible obs: 99.86 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.0335
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.8-1.97.070.89303904298199.51
1.9-2.017.110.53290614085199.78
2.01-2.157.150.34277313877199.93
2.15-2.327.210.2261063621199.99
2.32-2.557.290.132400132941100
2.55-2.857.340.092212830161100
2.85-3.297.340.051959826701100
3.29-4.027.240.041634422561100
4.02-5.697.270.031288217731100
5.69-307.060.027002992199.16

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
SHELXphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.54 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.951 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. The second data set attached is based on the same diffraction images as the refinement amplitudes but was ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. The second data set attached is based on the same diffraction images as the refinement amplitudes but was processed in HKL3000 and used for SAD phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1513 5.1 %THIN SHELLS (SFTOOLS)
Rwork0.2018 ---
obs0.2036 29857 99.78 %-
all-29923 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.12 Å2 / Biso mean: 27.0878 Å2 / Biso min: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å2-0.6 Å2
2--0.27 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 49 103 2223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222226
X-RAY DIFFRACTIONr_bond_other_d0.0010.021576
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9553015
X-RAY DIFFRACTIONr_angle_other_deg0.88133813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34922.897107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59115396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8321522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02484
X-RAY DIFFRACTIONr_mcbond_it0.6831.51336
X-RAY DIFFRACTIONr_mcbond_other0.1921.5542
X-RAY DIFFRACTIONr_mcangle_it1.19322167
X-RAY DIFFRACTIONr_scbond_it2.1463890
X-RAY DIFFRACTIONr_scangle_it3.3984.5839
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.327160.2812128216299.167
1.847-1.89700.2722135215099.302
1.897-1.9520.2852800.2461787207799.519
1.952-2.01100.2132003201099.652
2.011-2.0770.242300.2061747198499.647
2.077-2.1500.1941895189699.947
2.15-2.230.196200.191778179999.944
2.23-2.3210.2241970.1781594179299.944
2.321-2.4230.17860.1951666167399.94
2.423-2.540.231660.1921455162299.938
2.54-2.6770.2341390.1931413155399.936
2.677-2.83800.214491449100
2.838-3.0310.2561270.1961256138499.928
3.031-3.27100.212791279100
3.271-3.5790.2291050.18910991204100
3.579-3.9930.181680.178997106699.906
3.993-4.5960.198610.166904965100
4.596-5.5930.233400.193773813100
5.593-7.7620.307290.26462165199.846
7.762-28.5440.344290.26736539599.747
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)
11.3837-0.22310.7633.5139-1.66363.2265-0.006-0.04060.0672-0.0436-0.0439-0.1113-0.05510.11190.04980.00990.0034-0.00260.0153-0.01130.024823.631817.33842.3143
24.9482-0.1037-0.81481.91820.52643.84150.0838-0.1266-0.0229-0.1169-0.0834-0.1893-0.09090.2985-0.00040.0432-0.0073-0.00110.03960.02510.039741.5642-3.092359.9348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A348 - 482
2X-RAY DIFFRACTION2B350 - 482

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