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- PDB-2y8f: Structure of the Ran-binding domain from human RanBP3 (wild type) -

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Basic information

Entry
Database: PDB / ID: 2y8f
TitleStructure of the Ran-binding domain from human RanBP3 (wild type)
ComponentsRAN-BINDING PROTEIN 3
KeywordsPROTEIN TRANSPORT / CRM1-MEDIATED NUCLEAR EXPORT
Function / homology
Function and homology information


R-SMAD binding / nuclear pore / protein export from nucleus / small GTPase binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Ran-binding protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLanger, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C.
CitationJournal: Plos One / Year: 2011
Title: Insights Into the Function of the Crm1 Cofactor Ranbp3 from the Structure of its Ran-Binding Domain
Authors: Langer, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C.
History
DepositionFeb 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAN-BINDING PROTEIN 3
B: RAN-BINDING PROTEIN 3
C: RAN-BINDING PROTEIN 3
D: RAN-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,77911
Polymers62,1914
Non-polymers5887
Water4,414245
1
A: RAN-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8605
Polymers15,5481
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAN-BINDING PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)15,5481
Polymers15,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RAN-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6402
Polymers15,5481
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RAN-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7323
Polymers15,5481
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.902, 73.406, 120.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RAN-BINDING PROTEIN 3 / RANBP3-B


Mass: 15547.807 Da / Num. of mol.: 4 / Fragment: RAN BINDING DOMAIN, RESIDUES 320-454
Source method: isolated from a genetically manipulated source
Details: ISOFORM3 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6Z4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGAM REMAINING RESIDUES FROM TEV CLEAVAGE SITE

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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: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE
Crystal growpH: 7.5 / Details: 30% PEG 3350, 50 MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2009 / Details: TOROIDAL MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 33296 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 5.6 % / Biso Wilson estimate: 27.51 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.399 Å / SU ML: 0.31 / σ(F): 1.38 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1679 5.1 %
Rwork0.1914 --
obs0.193 33231 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.181 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 34.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.7089 Å20 Å20 Å2
2--2.0225 Å20 Å2
3---0.6864 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 37 245 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033853
X-RAY DIFFRACTIONf_angle_d0.6935164
X-RAY DIFFRACTIONf_dihedral_angle_d15.4971444
X-RAY DIFFRACTIONf_chiral_restr0.053614
X-RAY DIFFRACTIONf_plane_restr0.001643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.23931860.20963083X-RAY DIFFRACTION100
2.1751-2.26220.25751710.20263096X-RAY DIFFRACTION100
2.2622-2.36510.26491640.19643094X-RAY DIFFRACTION100
2.3651-2.48980.22951610.20163136X-RAY DIFFRACTION100
2.4898-2.64580.25681630.19753129X-RAY DIFFRACTION100
2.6458-2.850.24091720.20243144X-RAY DIFFRACTION100
2.85-3.13680.23681580.19213150X-RAY DIFFRACTION100
3.1368-3.59050.2021490.1813189X-RAY DIFFRACTION100
3.5905-4.5230.20272020.16383174X-RAY DIFFRACTION100
4.523-44.40860.2081530.23357X-RAY DIFFRACTION99
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)
10.9322-0.5017-0.47151.98380.0220.11040.0554-0.10990.06680.0881-0.0637-0.0042-0.0170.040200.0593-0.0117-0.00470.049-0.00850.043-10.52322.2218-17.408
20.7591-0.48640.70510.8508-0.08691.29080.19240.06530.0078-0.0536-0.106-0.06590.16990.355900.12850.0555-0.01080.1697-0.01480.1199-40.5712-10.4059-21.6403
30.85670.51230.01610.91460.14010.95470.0725-0.32320.1924-0.0495-0.0966-0.0132-0.0301-0.0598-00.0981-0.02640.02610.2217-0.08640.1029-33.72927.47821.0053
40.17840.30410.2780.82170.60.76680.0574-0.0169-0.0573-0.0265-0.0745-0.037-0.0314-0.0897-00.06560.00970.01280.06410.01620.0935-10.0737-21.4506-28.254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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