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- PDB-4qam: Crystal Structure of the RPGR RCC1-like domain in complex with th... -

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Basic information

Entry
Database: PDB / ID: 4qam
TitleCrystal Structure of the RPGR RCC1-like domain in complex with the RPGR-interacting domain of RPGRIP1
Components
  • X-linked retinitis pigmentosa GTPase regulator
  • X-linked retinitis pigmentosa GTPase regulator-interacting protein 1
KeywordsSIGNALING PROTEIN / type II C2 domain / beta propeller
Function / homology
Function and homology information


photoreceptor distal connecting cilium / intraciliary transport / photoreceptor connecting cilium / eye photoreceptor cell development / neural precursor cell proliferation / response to stimulus / axoneme / cilium assembly / photoreceptor outer segment / sperm flagellum ...photoreceptor distal connecting cilium / intraciliary transport / photoreceptor connecting cilium / eye photoreceptor cell development / neural precursor cell proliferation / response to stimulus / axoneme / cilium assembly / photoreceptor outer segment / sperm flagellum / visual perception / guanyl-nucleotide exchange factor activity / ciliary basal body / intracellular protein transport / ubiquitin protein ligase activity / retina development in camera-type eye / ubiquitin-dependent protein catabolic process / protein ubiquitination / centrosome / Golgi apparatus / RNA binding / cytoplasm
Similarity search - Function
Retinitis pigmentosa GTPase regulator-interacting protein 1 / RPGR-interacting protein 1, first C2 domain / RPGRIP1 family / RPGRIP1, C-terminal / First C2 domain of RPGR-interacting protein 1 / Retinitis pigmentosa G-protein regulator interacting C-terminal / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 ...Retinitis pigmentosa GTPase regulator-interacting protein 1 / RPGR-interacting protein 1, first C2 domain / RPGRIP1 family / RPGRIP1, C-terminal / First C2 domain of RPGR-interacting protein 1 / Retinitis pigmentosa G-protein regulator interacting C-terminal / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / C2 domain / C2 domain / C2 domain / C2 domain profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
X-linked retinitis pigmentosa GTPase regulator / X-linked retinitis pigmentosa GTPase regulator-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRemans, K. / Buerger, M. / Vetter, I.R. / Wittinghofer, A.
CitationJournal: Cell Rep / Year: 2014
Title: C2 domains as protein-protein interaction modules in the ciliary transition zone.
Authors: Remans, K. / Burger, M. / Vetter, I.R. / Wittinghofer, A.
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Experimental preparation
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: X-linked retinitis pigmentosa GTPase regulator
B: X-linked retinitis pigmentosa GTPase regulator-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,43111
Polymers66,7382
Non-polymers6939
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-18 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.120, 63.800, 161.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein X-linked retinitis pigmentosa GTPase regulator / RPGR


Mass: 43553.012 Da / Num. of mol.: 1 / Fragment: RCC1-like domain (UNP residues 1-392) / Mutation: V195I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RP3, RPGR, XLRP3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92834
#2: Protein X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 / RPGRIP1 / RPGR-interacting protein 1


Mass: 23185.064 Da / Num. of mol.: 1 / Fragment: RPGR-interacting domain (UNP residues 1091-1286)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPGRIP1 / Plasmid: pProEx Htb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q96KN7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG3350, 300 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.83→43.232 Å / Num. obs: 58347 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.282 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.13
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.83-1.880.9043.215678142341100
1.88-1.930.7154.135720141511100
1.93-1.980.5455.295535640491100
1.98-2.050.4286.715279439191100
2.05-2.110.3368.15012138061100
2.11-2.190.2699.644677337041100
2.19-2.270.21611.814696635481100
2.27-2.360.20212.964762134461100
2.36-2.470.17414.664522432931100
2.47-2.590.13917.624244931401100
2.59-2.730.11120.933977430371100
2.73-2.890.09324.293621828701100
2.89-3.090.07830.143718926741100
3.09-3.340.0637.713455225241100
3.34-3.660.04946.793091923061100
3.66-4.090.04251.172607121201100
4.09-4.730.03957.042443518851100
4.73-5.790.0457.582149916241100
5.79-8.180.04552.96150181264199.9
8.18-43.2320.03861.448813753199.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
PHENIXAutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JHN

4jhn


Resolution: 1.83→43.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1837 / WRfactor Rwork: 0.1504 / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8867 / SU B: 4.667 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1073 / SU Rfree: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 2917 5 %RANDOM
Rwork0.162 ---
obs0.1637 58343 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.05 Å2 / Biso mean: 32.961 Å2 / Biso min: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.83→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 44 322 4589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.024429
X-RAY DIFFRACTIONr_angle_refined_deg2.2351.9676005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9255567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24425.243206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32915734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7191516
X-RAY DIFFRACTIONr_chiral_restr0.1880.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213375
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 188 -
Rwork0.277 3755 -
all-3943 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.60950.2163-0.20541.29210.14240.9252-0.02230.03080.0128-0.29770.014-0.0098-0.0443-0.0080.00830.12450.00840.00390.01920.00550.0027-28.308-5.28614.997
20.45350.440.0691.53110.01151.7771-0.0381-0.0575-0.09970.18580.0156-0.3220.1190.31180.02250.06760.0315-0.02950.09030.00120.1104-21.152-1.13348.024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 504
2X-RAY DIFFRACTION2B1097 - 1283

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