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- PDB-9di4: RMI1-RMI2 bound to cyclic peptide L4 -

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Basic information

Entry
Database: PDB / ID: 9di4
TitleRMI1-RMI2 bound to cyclic peptide L4
Components
  • L4 cyclic peptide
  • RecQ-mediated genome instability protein 1
  • RecQ-mediated genome instability protein 2
KeywordsNUCLEAR PROTEIN / Nuclear protein complex / genome stability
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 speck / nuclear body / DNA repair / nucleotide binding / 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: 2.696 Å
AuthorsBythell-Douglas, R. / Lau, Y.H. / Alcock, L.J. / Gao, T. / Deshpande, C. / Patel, K.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Ideas APP2003250 Australia
National Health and Medical Research Council (NHMRC, Australia)MRFF MRF2007488 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
DepositionSep 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: 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: L4 cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5995
Polymers34,4683
Non-polymers1312
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-52 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.298, 136.298, 88.608
Angle α, β, γ (deg.)90, 90, 120
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-701-

ZN

21A-807-

HOH

31C-103-

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 L4 cyclic peptide


Mass: 1636.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 0.01M zinc chloride, 0.1M sodium acetate pH 5.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.69→49.169 Å / Num. obs: 13881 / % possible obs: 99.6 % / Redundancy: 38.8 % / CC1/2: 0.999 / Net I/σ(I): 22.2
Reflection shellResolution: 2.69→2.83 Å / Num. unique obs: 1742 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.696→49.169 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.245 / SU ML: 0.232 / Cross valid method: FREE R-VALUE / ESU R: 0.358 / ESU R Free: 0.286
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2482 673 4.856 %
Rwork0.1693 13185 -
all0.173 --
obs-13858 99.77 %
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: 61.815 Å2
Baniso -1Baniso -2Baniso -3
1--3.401 Å2-1.701 Å2-0 Å2
2---3.401 Å20 Å2
3---11.033 Å2
Refinement stepCycle: LAST / Resolution: 2.696→49.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 2 38 2321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162286
X-RAY DIFFRACTIONr_angle_refined_deg2.9791.8453150
X-RAY DIFFRACTIONr_angle_other_deg0.9341.7585281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9595291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72610417
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4831091
X-RAY DIFFRACTIONr_chiral_restr0.1130.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined0.2350.2410
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.22130
X-RAY DIFFRACTIONr_nbtor_refined0.1980.21104
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1040.21459
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1560.224
X-RAY DIFFRACTIONr_nbd_other0.1510.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0340.22
X-RAY DIFFRACTIONr_mcbond_it7.6445.7481176
X-RAY DIFFRACTIONr_mcbond_other7.6365.7471175
X-RAY DIFFRACTIONr_mcangle_it9.79410.3011465
X-RAY DIFFRACTIONr_mcangle_other9.78410.31465
X-RAY DIFFRACTIONr_scbond_it10.7326.4751151
X-RAY DIFFRACTIONr_scbond_other10.7286.4751152
X-RAY DIFFRACTIONr_scangle_it14.21911.4561685
X-RAY DIFFRACTIONr_scangle_other14.21511.4551686
X-RAY DIFFRACTIONr_lrange_it15.01852.9822406
X-RAY DIFFRACTIONr_lrange_other15.01952.9882405
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
2.696-2.7650.342410.3139290.3149950.870.9297.48740.289
2.765-2.8410.364570.2989230.3039800.9120.9331000.277
2.841-2.9230.298430.2748930.2759360.9250.9411000.246
2.923-3.0130.394360.2568940.269300.920.9551000.229
3.013-3.1110.311420.238570.2358990.930.9581000.206
3.111-3.220.308390.2138140.2178530.9340.9671000.192
3.22-3.3410.326550.197880.1998430.9250.9751000.172
3.341-3.4770.26480.1857630.1898110.9590.9811000.167
3.477-3.630.233300.1717480.1737790.9650.98499.87160.158
3.63-3.8070.277440.1667090.1737530.9540.9831000.155
3.807-4.0110.168350.1446820.1457170.9820.9881000.133
4.011-4.2530.175350.1166430.1196780.9810.9921000.11
4.253-4.5440.182210.1056270.1086480.9810.9931000.104
4.544-4.9040.203350.0955600.15950.9820.9941000.094
4.904-5.3670.157160.1125440.1135600.990.9921000.111
5.367-5.9920.194230.1484900.155130.9740.9881000.142
5.992-6.9020.259220.1744350.1784570.9630.9831000.165
6.902-8.4110.255270.1513720.1583990.9570.9831000.15
8.411-11.7250.166160.1513090.1513250.9860.9871000.158
11.725-49.1690.48580.2962050.3022130.8950.9421000.307

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