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- PDB-3nbh: Crystal structure of human RMI1C-RMI2 complex -

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Basic information

Entry
Database: PDB / ID: 3nbh
TitleCrystal structure of human RMI1C-RMI2 complex
Components
  • RecQ-mediated genome instability protein 1
  • RecQ-mediated genome instability protein 2
KeywordsPROTEIN BINDING / two OB-folds containing complex / RPA-like complex
Function / homology
Function and homology information


regulation of sister chromatid segregation / RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / maintenance of rDNA / resolution of meiotic recombination intermediates / Impaired BRCA2 binding to PALB2 / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function ...regulation of sister chromatid segregation / RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / maintenance of rDNA / resolution of meiotic recombination intermediates / Impaired BRCA2 binding to PALB2 / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of double-strand break repair via homologous recombination / response to glucose / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / multicellular organism growth / HDR through Homologous Recombination (HRR) / glucose homeostasis / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / nuclear body / nuclear speck / DNA repair / nucleotide binding / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #510 / Helix Hairpins - #770 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #510 / Helix Hairpins - #770 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Helix Hairpins / Nucleic acid-binding proteins / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWang, F. / Yang, Y. / Singh, T.R. / Busygina, V. / Guo, R. / Wan, K. / Wang, W. / Sung, P. / Meetei, A.R. / Lei, M.
CitationJournal: Structure / Year: 2010
Title: Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex.
Authors: Wang, F. / Yang, Y. / Singh, T.R. / Busygina, V. / Guo, R. / Wan, K. / Wang, W. / Sung, P. / Meetei, A.R. / Lei, M.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RecQ-mediated genome instability protein 1
B: RecQ-mediated genome instability protein 2


Theoretical massNumber of molelcules
Total (without water)33,6172
Polymers33,6172
Non-polymers00
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-19 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.682, 42.365, 157.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RecQ-mediated genome instability protein 1 / BLM-associated protein of 75 kDa / BLAP75 / FAAP75


Mass: 17453.371 Da / Num. of mol.: 1 / Fragment: RMI1C, residues 475-625
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28b-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H9A7
#2: Protein RecQ-mediated genome instability protein 2 / hRMI2 / BLM-associated protein of 18 kDa / BLAP18


Mass: 16163.621 Da / Num. of mol.: 1 / Fragment: RMI2, residues 6-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: GST-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96E14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The precipitant/well solution contained 18% PEG 3350, 300 mM NaSCN, and 10 mM DTT. , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 36368 / Num. obs: 35523 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 33.1
Reflection shellResolution: 2→2.03 Å / % possible all: 89.7

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3420 -RANDOM
Rwork0.215 ---
all-36447 --
obs-35460 97.3 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 0 373 2546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.63366
X-RAY DIFFRACTIONc_bond_d0.006436

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