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- PDB-9gwj: Crystal structure of CINP-c1orf109 complex -

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Basic information

Entry
Database: PDB / ID: 9gwj
TitleCrystal structure of CINP-c1orf109 complex
Components
  • AFG2-interacting ribosome maturation factor
  • Cyclin-dependent kinase 2-interacting protein
KeywordsSTRUCTURAL PROTEIN / hairpin / ribosome biogenesis
Function / homology
Function and homology information


preribosome binding / ribosomal large subunit biogenesis / DNA replication / cell division / DNA repair / nucleolus / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosome biogenesis protein C1orf109-like / Ribosome biogenesis protein C1orf109-like / Cyclin-dependent kinase 2-interacting protein
Similarity search - Domain/homology
Cyclin-dependent kinase 2-interacting protein / AFG2-interacting ribosome maturation factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.69 Å
AuthorsMasternak, M. / Weisser, M. / Montoya, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
CitationJournal: To Be Published
Title: Crystal structure of CINP-c1orf109 complex
Authors: Masternak, M. / Weisser, M. / Montoya, G.
History
DepositionSep 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AFG2-interacting ribosome maturation factor
B: Cyclin-dependent kinase 2-interacting protein
C: AFG2-interacting ribosome maturation factor
D: Cyclin-dependent kinase 2-interacting protein


Theoretical massNumber of molelcules
Total (without water)92,5544
Polymers92,5544
Non-polymers00
Water00
1
A: AFG2-interacting ribosome maturation factor
B: Cyclin-dependent kinase 2-interacting protein
C: AFG2-interacting ribosome maturation factor

D: Cyclin-dependent kinase 2-interacting protein


Theoretical massNumber of molelcules
Total (without water)92,5544
Polymers92,5544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)82.874, 115.166, 148.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1THRTHRGLUGLUAA2 - 2031 - 202
d_2ens_1THRTHRGLUGLUCC2 - 2031 - 202
d_1ens_2MSEMSELEULEUBB17 - 2121 - 196
d_2ens_2MSEMSELEULEUDD17 - 2121 - 196

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.749288644254, 0.661479257029, 0.0318075480421), (0.646086577804, 0.71961965607, 0.254400637931), (0.145391408183, 0.211169938955, -0.966575705937)-11.7288424904, -9.8445974557, 107.002597544
2given(0.717450651399, -0.694755858785, -0.0507824722759), (0.595432555339, 0.649451936262, -0.472940011554), (0.361558618829, 0.309073582129, 0.879629971056)60.3794089713, 52.4983228055, -37.7561023245

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Components

#1: Protein AFG2-interacting ribosome maturation factor / Ribosome biogenesis protein C1orf109


Mass: 23364.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIRIM, C1orf109 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NX04
#2: Protein Cyclin-dependent kinase 2-interacting protein / CDK2-interacting protein


Mass: 22912.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N terminal truncation: 1-17 aa / Source: (gene. exp.) Homo sapiens (human) / Gene: CINP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BW66
Has ligand of interestN
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: 3.87 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.236M sodium citrate, 23.4% 2-propanol, 0.1M sodium cacodylate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.69→49.92 Å / Num. obs: 15894 / % possible obs: 99.8 % / Redundancy: 25.3 % / Biso Wilson estimate: 168.35 Å2 / CC1/2: 0.9991 / Rmerge(I) obs: 0.411 / Net I/σ(I): 8.277
Reflection shellResolution: 3.69→3.82 Å / Redundancy: 17.29 % / Rmerge(I) obs: 6.252 / Mean I/σ(I) obs: 0.665 / Num. unique obs: 1552 / CC1/2: 0.1765 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.69→49.92 Å / SU ML: 0.7429 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.2343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.298 795 5 %
Rwork0.2651 15099 -
obs0.2667 15894 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 194.68 Å2
Refinement stepCycle: LAST / Resolution: 3.69→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6460 0 0 0 6460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00186582
X-RAY DIFFRACTIONf_angle_d0.43698906
X-RAY DIFFRACTIONf_chiral_restr0.03211008
X-RAY DIFFRACTIONf_plane_restr0.00371140
X-RAY DIFFRACTIONf_dihedral_angle_d12.0252504
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.40053441292
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.76527939732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.69-3.920.43471300.43052470X-RAY DIFFRACTION99.31
3.92-4.220.3591300.33012463X-RAY DIFFRACTION99.92
4.22-4.650.33141310.28512490X-RAY DIFFRACTION99.92
4.65-5.320.28141320.26612494X-RAY DIFFRACTION99.89
5.32-6.70.34181340.32532531X-RAY DIFFRACTION100
6.7-49.920.25391380.21252651X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 1.38038918721 Å / Origin y: 51.6580941157 Å / Origin z: 66.1198886191 Å
111213212223313233
T1.55305868007 Å2-0.073330636547 Å2-0.000208064783747 Å2-1.47342892804 Å20.0478692058338 Å2--1.29945336861 Å2
L0.12004189453 °2-0.254299800713 °2-0.324014437515 °2-0.110747347008 °20.417391235236 °2--0.30950606723 °2
S0.0462538720635 Å °0.0125241019286 Å °-0.111718539982 Å °0.0393814226713 Å °-0.0314177217586 Å °0.0052318078199 Å °0.17170344712 Å °0.231187723142 Å °-3.07391822924E-5 Å °
Refinement TLS groupSelection details: all

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