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- PDB-6fm8: RPAP3 c-terminus -

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Basic information

Entry
Database: PDB / ID: 6fm8
TitleRPAP3 c-terminus
ComponentsRNA polymerase II-associated protein 3
KeywordsPROTEIN BINDING / Co-chaperone / polymerase
Function / homology
Function and homology information


R2TP complex / RPAP3/R2TP/prefoldin-like complex / protein folding chaperone complex / protein stabilization / cytosol
Similarity search - Function
RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RNA polymerase II-associated protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsPal, M. / Roe, S.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex
Authors: Pal, M. / Roe, S.M.
History
DepositionJan 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II-associated protein 3


Theoretical massNumber of molelcules
Total (without water)6,1451
Polymers6,1451
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.631, 39.631, 70.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-740-

HOH

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Components

#1: Protein/peptide RNA polymerase II-associated protein 3


Mass: 6145.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPAP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6T3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.51 Å3/Da / Density % sol: 51 % / Description: Tetragonal bipyramidal
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.5M Potassium thiocyanate, 0.1M Bis-Tris Propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.78→70.4 Å / Num. obs: 5844 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 28.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.039 / Net I/σ(I): 8.9
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 418 / CC1/2: 0.505 / Rpim(I) all: 0.297 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
xia2data scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: helix

Resolution: 1.78→34.54 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.27 302 5.27 %RANDOM
Rwork0.231 ---
obs0.233 5727 98.5 %-
Displacement parametersBiso mean: 36.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.8147 Å20 Å20 Å2
2---1.8147 Å20 Å2
3---3.6294 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 1.78→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms393 0 0 41 434
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01412HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.09561HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d197SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes11HARMONIC2
X-RAY DIFFRACTIONt_gen_planes59HARMONIC5
X-RAY DIFFRACTIONt_it412HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion2.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion57SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact563SEMIHARMONIC4
LS refinement shellResolution: 1.78→1.99 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3325 -4.69 %
Rwork0.2808 1485 -
all0.2833 1558 -
obs--96.95 %

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