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- PDB-1i2m: RAN-RCC1-SO4 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i2m
TitleRAN-RCC1-SO4 COMPLEX
Components
  • GTP-BINDING NUCLEAR PROTEIN RAN
  • REGULATOR OF CHROMOSOME CONDENSATION 1
KeywordsCELL CYCLE / beta-propeller / G fold or GTPase fold
Function / homology
Function and homology information


pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / sulfate binding / mitotic nuclear membrane reassembly / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA ...pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / sulfate binding / mitotic nuclear membrane reassembly / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / regulation of mitotic spindle assembly / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nucleosomal DNA binding / DNA metabolic process / regulation of mitotic nuclear division / dynein intermediate chain binding / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / spermatid development / viral process / positive regulation of protein binding / sperm flagellum / nuclear pore / ribosomal subunit export from nucleus / nucleosome binding / spindle assembly / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / regulation of mitotic cell cycle / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / mitotic spindle organization / male germ cell nucleus / hippocampus development / chromosome segregation / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / recycling endosome / positive regulation of protein import into nucleus / small GTPase binding / protein import into nucleus / GDP binding / melanosome / nuclear envelope / mitotic cell cycle / chromosome / G protein activity / actin cytoskeleton organization / midbody / histone binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / : / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Ran GTPase ...Regulator of chromosome condensation (RCC1) signature 1. / : / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Ran GTPase / Small GTPase Ran-type domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 7 Propeller / Methylamine Dehydrogenase; Chain H / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Regulator of chromosome condensation / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsRenault, L. / Kuhlmann, J. / Henkel, A. / Wittinghofer, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural basis for guanine nucleotide exchange on Ran by the regulator of chromosome condensation (RCC1).
Authors: Renault, L. / Kuhlmann, J. / Henkel, A. / Wittinghofer, A.
History
DepositionFeb 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Aug 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-BINDING NUCLEAR PROTEIN RAN
B: REGULATOR OF CHROMOSOME CONDENSATION 1
C: GTP-BINDING NUCLEAR PROTEIN RAN
D: REGULATOR OF CHROMOSOME CONDENSATION 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9396
Polymers134,7474
Non-polymers1922
Water8,557475
1
A: GTP-BINDING NUCLEAR PROTEIN RAN
B: REGULATOR OF CHROMOSOME CONDENSATION 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4703
Polymers67,3742
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-19 kcal/mol
Surface area21570 Å2
MethodPISA
2
C: GTP-BINDING NUCLEAR PROTEIN RAN
D: REGULATOR OF CHROMOSOME CONDENSATION 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4703
Polymers67,3742
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-19 kcal/mol
Surface area21780 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-52 kcal/mol
Surface area40970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.334, 71.447, 77.729
Angle α, β, γ (deg.)100.92, 92.05, 104.47
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GTP-BINDING NUCLEAR PROTEIN RAN / RAN


Mass: 24456.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62826
#2: Protein REGULATOR OF CHROMOSOME CONDENSATION 1 / RCC1


Mass: 42917.402 Da / Num. of mol.: 2
Fragment: PROTEIN TRUNCATED FROM THE N-TERMINAL RESIDUES 1 TO 19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTAC / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P18754
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-10% PEG 4000, 200 mM potassium fluoride, 25 mM potassium phosphate, 25 mM ammonium sulfate, 2 mM EDTA, 3mM DTE, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG33501reservoir
2200 mMKF1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.9801
SYNCHROTRONESRF ID220.9903
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEJun 26, 1999mirrors
MARRESEARCH2IMAGE PLATEJul 14, 1999mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 and 311 single crystalsSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.98011
20.99031
ReflectionResolution: 1.63→19.79 Å / Num. all: 123475 / Num. obs: 484600 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 23.7 Å2 / Limit h max: 30 / Limit h min: -30 / Limit k max: 42 / Limit k min: -30 / Limit l max: 47 / Limit l min: 0 / Observed criterion F max: 156076284.73 / Observed criterion F min: 1060.6 / Rmerge(I) obs: 0.146 / Net I/σ(I): 6.8
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 0.8 / % possible all: 56.1
Reflection shell
*PLUS
% possible obs: 56.1 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A12 (RCC1) and human Ran-GDP-Mg2+ structure (Scheffzek, K. et al. (1995))

1a12


Resolution: 1.76→19.79 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 8466 8.3 %RANDOM
Rwork0.192 ---
all-101671 --
obs-101433 99.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.116 Å2 / ksol: 0.375011 e/Å3
Displacement parametersBiso max: 99.12 Å2 / Biso mean: 35.55 Å2 / Biso min: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å21.41 Å20.77 Å2
2---3.2 Å2-0.23 Å2
3---4.75 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Luzzati d res high-1.76
Refinement stepCycle: LAST / Resolution: 1.76→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8499 0 10 475 8984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg25.6
X-RAY DIFFRACTIONx_torsion_impr_deg0.73
X-RAY DIFFRACTIONx_mcbond_it3.081.5
X-RAY DIFFRACTIONx_mcangle_it5.022
X-RAY DIFFRACTIONx_scbond_it4.762
X-RAY DIFFRACTIONx_scangle_it7.822.5
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.76-1.790.33144178.40.304344870.0155120506398.9
1.79-1.820.30554398.60.293146510.0145092504799.1
1.82-1.860.28914498.80.268446560.0135166513299.3
1.86-1.890.27984398.50.244846120.0125055502299.3
1.89-1.940.26234378.50.228847070.0115176514099.3
1.94-1.980.25214048.10.217146650.0115076505999.6
1.98-2.030.26544458.60.242146090.0125098506499.3
2.03-2.090.23863987.70.210146940.0115093507699.7
2.09-2.150.24434148.10.246400.015065504099.5
2.15-2.220.22384268.30.192146960.0095139512099.6
2.22-2.290.23414238.30.200246940.015120511099.8
2.29-2.390.27834097.90.211646780.0115092508199.8
2.39-2.490.25014007.90.203546830.015088507699.8
2.49-2.630.21784228.30.191546450.0095070506099.8
2.63-2.790.22544178.10.183846730.0095094508899.9
2.79-3.010.22624298.50.189446460.0095063505799.9
3.01-3.310.20734268.40.178546520.0095090507899.8
3.31-3.780.19714468.70.169946320.0085084505599.4
3.78-4.750.1754358.50.152946080.0075091504599.1
4.75-19.80.2213917.70.194446390.015084502098.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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