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- PDB-9pfd: RMI1-RMI2 bound to synthetic peptide P4Ser -

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Basic information

Entry
Database: PDB / ID: 9pfd
TitleRMI1-RMI2 bound to synthetic peptide P4Ser
Components
  • P4Ser peptide
  • RecQ-mediated genome instability protein 1
  • RecQ-mediated genome instability protein 2
KeywordsNUCLEAR PROTEIN / 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 / response to glucose / negative regulation of double-strand break repair via homologous recombination / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / multicellular organism growth / glucose homeostasis / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / nuclear speck / nuclear body / nucleotide binding / DNA repair / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 ...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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RecQ-mediated genome instability protein 2 / RecQ-mediated genome instability protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.008 Å
AuthorsBythell-Douglas, R. / Lau, Y.H. / Alcock, L.J. / Deshpande, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Med.Chem. / Year: 2025
Title: Potent Cyclic Peptide Inhibitors Disrupt the FANCM-RMI Interaction.
Authors: Alcock, L.J. / Gao, T. / Bythell-Douglas, R. / Gao, J. / Krishna Sudhakar, H. / Huang, T. / Young, R. / Vu, Q.N. / Deshpande, C. / Wilkinson-White, L.E. / Passioura, T. / Pickett, H.A. / Deans, A.J. / Lau, Y.H.
History
DepositionJul 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RecQ-mediated genome instability protein 1
B: RecQ-mediated genome instability protein 2
C: P4Ser peptide


Theoretical massNumber of molelcules
Total (without water)34,4973
Polymers34,4973
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-36 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.541, 117.541, 53.475
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-784-

HOH

21B-241-

HOH

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Components

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


Mass: 16944.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMI1, C9orf76 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9A7
#2: Protein RecQ-mediated genome instability protein 2 / hRMI2 / BLM-associated protein of 18 kDa / BLAP18


Mass: 15886.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMI2, C16orf75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96E14
#3: Protein/peptide P4Ser peptide


Mass: 1665.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.008→48.772 Å / Num. obs: 25632 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Net I/σ(I): 35.2
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 1866 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.008→48.722 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.84 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.152 / ESU R Free: 0.145
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2241 1335 5.218 %
Rwork0.181 24249 -
all0.183 --
obs-25584 99.973 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.802 Å2
Baniso -1Baniso -2Baniso -3
1--1.063 Å20 Å20 Å2
2---1.063 Å20 Å2
3---2.126 Å2
Refinement stepCycle: LAST / Resolution: 2.008→48.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 1 170 2421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122315
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162318
X-RAY DIFFRACTIONr_angle_refined_deg2.4421.843142
X-RAY DIFFRACTIONr_angle_other_deg0.8181.7665290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5325293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.396517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33110403
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg11.374106
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5881089
X-RAY DIFFRACTIONr_chiral_restr0.1220.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
X-RAY DIFFRACTIONr_nbd_refined0.2270.2431
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22135
X-RAY DIFFRACTIONr_nbtor_refined0.190.21118
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.21371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.140.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.24
X-RAY DIFFRACTIONr_nbd_other0.1460.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.218
X-RAY DIFFRACTIONr_mcbond_it4.5873.2531176
X-RAY DIFFRACTIONr_mcbond_other4.5893.2521175
X-RAY DIFFRACTIONr_mcangle_it5.9235.7851469
X-RAY DIFFRACTIONr_mcangle_other5.9255.7851469
X-RAY DIFFRACTIONr_scbond_it6.2863.8391139
X-RAY DIFFRACTIONr_scbond_other6.2833.8391140
X-RAY DIFFRACTIONr_scangle_it8.9076.7341673
X-RAY DIFFRACTIONr_scangle_other8.9046.7331674
X-RAY DIFFRACTIONr_lrange_it10.57231.5642528
X-RAY DIFFRACTIONr_lrange_other10.58931.2142501
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.008-2.060.288960.23517670.23818670.9480.96499.78580.206
2.06-2.1170.295760.22817270.23118030.9360.9671000.204
2.117-2.1780.292950.23416610.23717560.9460.9631000.209
2.178-2.2450.287830.21216270.21617100.940.9711000.191
2.245-2.3180.218820.19415720.19616540.9680.9771000.178
2.318-2.3990.256820.20915260.21116080.9550.9741000.188
2.399-2.490.269860.20514710.20815570.9490.9731000.188
2.49-2.5910.261870.21113980.21314850.9540.9721000.193
2.591-2.7060.223580.19613970.19714550.9670.9751000.184
2.706-2.8380.25720.19313140.19613860.9660.9771000.182
2.838-2.9910.2730.19212390.19313120.9750.9771000.184
2.991-3.1710.209750.19411850.19512600.9690.9771000.19
3.171-3.3890.272680.19411130.19811810.9560.9761000.195
3.389-3.6590.232520.18310440.18510960.9710.9811000.185
3.659-4.0060.216600.1799690.18110290.9740.9821000.185
4.006-4.4750.178480.1418900.1429380.9820.9891000.152
4.475-5.1610.143380.1257990.1268370.9850.9921000.139
5.161-6.3030.189490.1436600.1477090.9850.991000.154
6.303-8.840.205350.1535500.1565850.9860.9881000.165
8.84-48.7220.21200.1583400.1613600.9650.9811000.176

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