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- PDB-5uwq: Crystal Structure of CDC7 NES Peptide in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 5uwq
TitleCrystal Structure of CDC7 NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Cell division cycle 7-related protein kinase
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


positive regulation of nuclear cell cycle DNA replication / MAPK6/MAPK4 signaling / cell cycle phase transition / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) ...positive regulation of nuclear cell cycle DNA replication / MAPK6/MAPK4 signaling / cell cycle phase transition / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / double-strand break repair via break-induced replication / U4 snRNA binding / RNA export from nucleus / spindle pole body / protein localization to kinetochore / nuclear export / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / NLS-bearing protein import into nucleus / dynein intermediate chain binding / intercellular bridge / ribosomal subunit export from nucleus / Transcriptional Regulation by E2F6 / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / Activation of the pre-replicative complex / U5 snRNA binding / sperm flagellum / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / Activation of ATR in response to replication stress / nuclear pore / U1 snRNA binding / positive regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / centriole / viral process / GTPase activator activity / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G1/S transition of mitotic cell cycle / mitotic spindle / kinetochore / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / kinase activity / midbody / ubiquitin-dependent protein catabolic process / actin cytoskeleton organization / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / phosphorylation / protein serine kinase activity / GTPase activity / protein serine/threonine kinase activity / chromatin binding / positive regulation of cell population proliferation / chromatin / GTP binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / signal transduction / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division cycle 7-related protein kinase / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.278 Å
AuthorsFung, H.Y.J. / Chook, Y.M.
Funding support United States, Hong Kong, 7items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)International Student Research Fellowship United States
Croucher FoundationPredoc Research Scholarship Hong Kong
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award United States
University of Texas Southwestern Medical CenterEndowed Scholars Program United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352, RP150053 United States
CitationJournal: Elife / Year: 2017
Title: Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals.
Authors: Fung, H.Y. / Fu, S.C. / Chook, Y.M.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
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.ptnr2_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: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: Cell division cycle 7-related protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,12810
Polymers163,2134
Non-polymers9156
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-49 kcal/mol
Surface area58330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.392, 106.392, 304.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1103-

GOL

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 26758.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16521.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920
#3: Protein Exportin-1 / Karyopherin / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117458.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Cell division cycle 7-related protein kinase /


Mass: 2473.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00311*PLUS

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Non-polymers , 4 types, 522 molecules

#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 16% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 8 mM HCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 80110 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.038 / Net I/σ(I): 20.5
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3899 / CC1/2: 0.578 / Rpim(I) all: 0.542 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HB2

4hb2


Resolution: 2.278→40.272 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 1999 2.59 %
Rwork0.1853 --
obs0.1863 77109 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.278→40.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 24 516 11472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211355
X-RAY DIFFRACTIONf_angle_d0.53515373
X-RAY DIFFRACTIONf_dihedral_angle_d15.6626905
X-RAY DIFFRACTIONf_chiral_restr0.0381745
X-RAY DIFFRACTIONf_plane_restr0.0031958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2784-2.33540.31181010.24383800X-RAY DIFFRACTION69
2.3354-2.39850.31831320.23864948X-RAY DIFFRACTION89
2.3985-2.46910.27891350.22095094X-RAY DIFFRACTION92
2.4691-2.54880.26871380.21055169X-RAY DIFFRACTION93
2.5488-2.63980.26771440.20595401X-RAY DIFFRACTION97
2.6398-2.74550.23961460.2095451X-RAY DIFFRACTION99
2.7455-2.87040.26191480.20045560X-RAY DIFFRACTION99
2.8704-3.02170.24591460.19795543X-RAY DIFFRACTION99
3.0217-3.2110.26441490.20265548X-RAY DIFFRACTION99
3.211-3.45880.23311480.19055577X-RAY DIFFRACTION99
3.4588-3.80660.19291500.17135627X-RAY DIFFRACTION100
3.8066-4.35690.18731500.1585655X-RAY DIFFRACTION100
4.3569-5.4870.1911530.14745759X-RAY DIFFRACTION100
5.487-40.27830.1981590.18535978X-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)
10.7749-0.1635-0.15451.2851-0.42160.57790.04150.1698-0.05-0.17560.1605-0.453-0.2930.3485-0.09450.2385-0.09160.06510.3297-0.11150.37669.121448.701232.9537
21.3416-0.5742-0.10120.7312-0.11050.86750.05240.0264-0.31640.12060.0571-0.3820.16660.1427-0.03020.1435-0.0087-0.02780.2846-0.09920.41868.076337.261937.0886
31.37290.111-0.1122.1393-0.15311.77610.02330.041-0.1237-0.23680.0477-0.03870.0237-0.1277-0.04790.15050.0003-0.02010.2266-0.06320.2325-4.809741.739137.1637
40.0913-0.05990.2920.714-0.46670.96360.06830.1538-0.0063-0.09590.0902-0.2036-0.59130.4439-0.07080.4667-0.19250.10180.5088-0.13920.42868.581261.48523.8189
50.0140.0183-0.01730.0134-0.00280.02020.0473-0.11510.0568-0.2590.39660.023-0.3878-0.1197-0.14381.1273-0.22060.11550.92350.01090.83270.340184.062754.4751
61.8782-0.22530.01012.69130.30631.7153-0.0496-0.02060.00420.24590.0891-0.087-0.06640.4429-0.02050.4889-0.13790.1470.3631-0.02510.40226.801563.291817.3883
70.36080.03370.19090.70060.23040.21830.01630.02980.1369-0.1553-0.05560.0845-0.69490.42740.08760.78-0.30630.18070.463-0.04940.48827.324671.37419.5468
81.85211.0458-0.10131.91540.83370.8678-0.02380.0880.1114-0.22640.12380.1168-0.76340.42580.03250.6485-0.2330.12310.4463-0.03850.46687.668771.421513.7495
90.9597-0.1169-0.03631.39840.4361.0165-0.0486-0.14520.00030.54880.2174-0.56280.33540.3244-0.00730.23910.1145-0.16470.324-0.05820.46587.275225.590253.7285
101.2139-0.6160.66151.0471-0.40012.88530.06060.08330.05750.0160.0213-0.0146-0.2832-0.2253-0.07090.19850.01770.02790.2614-0.05320.1768-26.266654.175648.0273
111.9835-0.8493-0.77221.18920.32911.92820.06190.07610.1437-0.09970.1435-0.0426-0.561-0.2927-0.08960.36820.11610.05620.34010.04970.1974-26.530455.57074.246
120.8066-0.55160.70521.0329-1.21381.8290.09590.0886-0.2701-0.080.0670.15650.06760.0691-0.10730.21640.02470.02280.266-0.08050.3102-8.801517.303714.6356
131.02590.5630.99393.7678-0.22522.02890.04620.14610.3599-0.2258-0.10360.3787-0.16980.0079-0.02561.20280.56130.01980.77710.03470.7595-41.33275.733728.4482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 216 )
5X-RAY DIFFRACTION5chain 'B' and (resid 63 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 106 )
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 154 )
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 200 )
9X-RAY DIFFRACTION9chain 'C' and (resid 0 through 268 )
10X-RAY DIFFRACTION10chain 'C' and (resid 269 through 569 )
11X-RAY DIFFRACTION11chain 'C' and (resid 570 through 808 )
12X-RAY DIFFRACTION12chain 'C' and (resid 809 through 1053 )
13X-RAY DIFFRACTION13chain 'D' and (resid 456 through 468 )

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