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- PDB-4oo6: Crystal structure of human KAP-beta2 bound to the NLS of HCC1 (He... -

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Basic information

Entry
Database: PDB / ID: 4oo6
TitleCrystal structure of human KAP-beta2 bound to the NLS of HCC1 (Hepato Cellular Carcinoma protein 1)
Components
  • RNA-binding protein 39
  • Transportin-1
KeywordsTransport Protein/RNA Binding Protein / KARYOPHERIN / TRNAPORTIN / IMPORTIN / HEAT REPEATS / NUCLEAR IMPORT / PROTEIN TRANSPORT / NLS / Nuclear Localization Signal / RNA-binding protein / HCC1 / NUCLEOCYTOPLASMIC TRANSPORT: A TARGET FOR CELLULAR CONTROL (NPCXSTALS) / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC) / PSI-Biology / Transport Protein-RNA Binding Protein complex / NPCXstals
Function / homology
Function and homology information


RS domain binding / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / centriolar satellite / RNA processing ...RS domain binding / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / RNA splicing / cilium / mRNA processing / small GTPase binding / protein import into nucleus / microtubule cytoskeleton / nuclear speck / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / RNA recognition motif domain, eukaryote / RNA recognition motif / Importin-beta N-terminal domain profile. ...Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / RNA recognition motif domain, eukaryote / RNA recognition motif / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
RNA-binding protein 39 / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSampathkumar, P. / Brower, A. / Soniat, M. / Bonanno, J. / Hillerich, B. / Seidel, R.D. / Rout, M.P. / Chook, Y.M. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)
CitationJournal: to be published
Title: Crystal structure of human KAP-beta2 bound to the NLS of HCC1 (Hepato Cellular Carcinoma protein 1)
Authors: Sampathkumar, P. / Brower, A. / Soniat, M. / Bonanno, J. / Hillerich, B. / Seidel, R.D. / Rout, M.P. / Chook, Y.M. / Almo, S.C.
History
DepositionJan 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transportin-1
B: RNA-binding protein 39


Theoretical massNumber of molelcules
Total (without water)100,3522
Polymers100,3522
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-4 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.584, 162.152, 68.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological hetreo-dimer formed by Kap-Beta2 (chain A) and HCC1-NLS (chain B)

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Components

#1: Protein Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 96766.773 Da / Num. of mol.: 1 / Fragment: UNP residues 9-331 and 375-898
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB2, MIP1, TNPO1, TRN / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL CodonPlus / References: UniProt: Q92973
#2: Protein/peptide RNA-binding protein 39 / Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing ...Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Splicing factor HCC1


Mass: 3585.071 Da / Num. of mol.: 1 / Fragment: UNP residues 73-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCC1, RBM39, RNPC2 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL CodonPlus / References: UniProt: Q14498
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: "Protein (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACET ATE, 20% GLYCEROL, 2MM DTT); Reservoir (0.2 M Sodiumchloride, 0.8M Sodiumcitrate, 0.1M BisTris pH 6.25 ); Cryo (2. ...Details: "Protein (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACET ATE, 20% GLYCEROL, 2MM DTT); Reservoir (0.2 M Sodiumchloride, 0.8M Sodiumcitrate, 0.1M BisTris pH 6.25 ); Cryo (2.5 M Sodiummalonate)">, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2013 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 39520 / Num. obs: 39520 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.81 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4389 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FDD

4fdd


Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.613 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 1977 5 %RANDOM
Rwork0.1886 ---
obs0.1912 39470 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 170.93 Å2 / Biso mean: 67.545 Å2 / Biso min: 31.91 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å20 Å2-0 Å2
2--3.52 Å2-0 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6735 0 0 18 6753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196880
X-RAY DIFFRACTIONr_bond_other_d0.0020.026699
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9779343
X-RAY DIFFRACTIONr_angle_other_deg0.825315440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.11725310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.998151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3891534
X-RAY DIFFRACTIONr_chiral_restr0.0790.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021512
X-RAY DIFFRACTIONr_mcbond_it4.2626.3643373
X-RAY DIFFRACTIONr_mcbond_other4.2616.3643372
X-RAY DIFFRACTIONr_mcangle_it6.5219.5454211
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 147 -
Rwork0.35 2718 -
all-2865 -
obs-2718 99.58 %

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