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- PDB-4mqv: Crystal complex of Rpa32c and Smarcal1 N-terminus -

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Basic information

Entry
Database: PDB / ID: 4mqv
TitleCrystal complex of Rpa32c and Smarcal1 N-terminus
Components
  • Replication protein A 32 kDa subunit
  • SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
KeywordsPROTEIN BINDING / Winged HTH Fold / Nucleus
Function / homology
Function and homology information


DNA rewinding / : / protein localization to chromosome / DNA replication factor A complex / t-circle formation / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand ...DNA rewinding / : / protein localization to chromosome / DNA replication factor A complex / t-circle formation / regulation of DNA damage checkpoint / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / ATP-dependent DNA/DNA annealing activity / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / replication fork processing / nuclear replication fork / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / ATP-dependent activity, acting on DNA / mismatch repair / Activation of ATR in response to replication stress / DNA helicase activity / mitotic G1 DNA damage checkpoint signaling / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / double-strand break repair via nonhomologous end joining / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / site of double-strand break / single-stranded DNA binding / Processing of DNA double-strand break ends / protein phosphatase binding / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA repair / ubiquitin protein ligase binding / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
HARP domain / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 / HepA-related protein (HARP) / HARP domain profile. / Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein-like / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal ...HARP domain / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 / HepA-related protein (HARP) / HARP domain profile. / Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein-like / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Replication protein A 32 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsXie, S. / Qian, C.M.
CitationJournal: Febs J. / Year: 2014
Title: Structure of RPA32 bound to the N-terminus of SMARCAL1 redefines the binding interface between RPA32 and its interacting proteins
Authors: Xie, S. / Lu, Y. / Jakoncic, J. / Sun, H. / Xia, J. / Qian, C.M.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication protein A 32 kDa subunit
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
C: Replication protein A 32 kDa subunit
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,5644
Polymers21,5644
Non-polymers00
Water2,288127
1
A: Replication protein A 32 kDa subunit
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,7822
Polymers10,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-4 kcal/mol
Surface area5720 Å2
MethodPISA
2
C: Replication protein A 32 kDa subunit
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,7822
Polymers10,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-4 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.089, 149.089, 46.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11B-116-

HOH

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Components

#1: Protein Replication protein A 32 kDa subunit / RP-A p32 / Replication factor A protein 2 / RF-A protein 2 / Replication protein A 34 kDa subunit / RP-A p34


Mass: 7651.493 Da / Num. of mol.: 2 / Fragment: C-Terminal domain, UNP residues 202-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA32 / Production host: Escherichia Coli (E. coli) / References: UniProt: P15927
#2: Protein/peptide SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 / HepA-related protein / hHARP / Sucrose nonfermenting protein 2-like 1


Mass: 3130.644 Da / Num. of mol.: 2 / Fragment: N-Terminal peptide, UNP residues 5-30 / Source method: obtained synthetically / Details: This Sequence occurs naturally in Humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NZC9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 25% PEG 4000, 0.2M Sodium Acetate, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 21338 / Num. obs: 21338 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.95 Å / % possible all: 94.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0087refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.59 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.687 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1148 5.1 %RANDOM
Rwork0.192 ---
all0.193 22503 --
obs0.193 21338 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 127 1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9632035
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8425190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20425.32577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94715305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.311511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021125
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1371.5934
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11321505
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3513579
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6144.5528
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 88 -
Rwork0.211 1543 -
obs--100 %

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