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- PDB-5uwr: Crystal Structure of CDC7 NES Peptide (extended) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5uwr
TitleCrystal Structure of CDC7 NES Peptide (extended) in complex with CRM1-Ran-RanBP1
Components
  • Cell division cycle 7-related protein kinase
  • Exportin-1
  • 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 / cell cycle phase transition / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / Transcriptional and post-translational regulation of MITF-M expression and activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity ...positive regulation of nuclear cell cycle DNA replication / cell cycle phase transition / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / pre-miRNA export from nucleus / RNA nuclear export complex / Transcriptional and post-translational regulation of MITF-M expression and activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / spindle pole body / double-strand break repair via break-induced replication / Nuclear import of Rev protein / nuclear export / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / MAPK6/MAPK4 signaling / Transcriptional Regulation by E2F6 / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / U5 snRNA binding / Activation of the pre-replicative complex / viral process / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / Activation of ATR in response to replication stress / intercellular bridge / U1 snRNA binding / ribosomal small subunit export from nucleus / positive regulation of G2/M transition of mitotic cell cycle / centriole / GTPase activator activity / protein export from nucleus / mitotic spindle organization / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / kinetochore / G1/S transition of mitotic cell cycle / positive regulation of protein import into nucleus / protein import into nucleus / mitotic spindle / GDP binding / kinase activity / positive regulation of protein binding / nuclear envelope / melanosome / mitotic cell cycle / G protein activity / midbody / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein heterodimerization activity / cell division / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / positive regulation of cell population proliferation / chromatin binding
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / 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 / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / 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 / Roll / P-loop containing nucleotide triphosphate hydrolases / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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: 2.24 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 / Category: pdbx_audit_support / 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)164,61710
Polymers163,7594
Non-polymers8586
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-65 kcal/mol
Surface area57360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.085, 106.085, 304.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 / 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 / huCdc7


Mass: 3019.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7, CDC7L1 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00311

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Non-polymers , 5 types, 528 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 10 mM spermine-HCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 84118 / % possible obs: 99.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Net I/σ(I): 23.8
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4085 / Num. unique obs: 4085 / CC1/2: 0.384 / Rpim(I) all: 0.503 / % possible all: 99

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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: 2.24→47.443 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 2000 2.53 %
Rwork0.187 --
obs0.1879 79116 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→47.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10885 0 19 522 11426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311240
X-RAY DIFFRACTIONf_angle_d0.52715213
X-RAY DIFFRACTIONf_dihedral_angle_d15.4926834
X-RAY DIFFRACTIONf_chiral_restr0.0381729
X-RAY DIFFRACTIONf_plane_restr0.0031934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2397-2.29570.2743890.24983436X-RAY DIFFRACTION60
2.2957-2.35770.27071190.23084561X-RAY DIFFRACTION78
2.3577-2.42710.27961320.22075115X-RAY DIFFRACTION88
2.4271-2.50540.30481400.21635377X-RAY DIFFRACTION93
2.5054-2.5950.26911430.21115537X-RAY DIFFRACTION95
2.595-2.69890.25511470.20715666X-RAY DIFFRACTION97
2.6989-2.82170.24241480.2115752X-RAY DIFFRACTION99
2.8217-2.97040.24711520.20025813X-RAY DIFFRACTION100
2.9704-3.15650.25581520.20285847X-RAY DIFFRACTION100
3.1565-3.40020.20671520.19645892X-RAY DIFFRACTION100
3.4002-3.74220.22841530.17555888X-RAY DIFFRACTION100
3.7422-4.28340.18681540.15685956X-RAY DIFFRACTION100
4.2834-5.39540.17171560.14916011X-RAY DIFFRACTION100
5.3954-47.45330.20081630.18756265X-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)
10.5973-0.5933-0.20350.76590.49412.1975-0.0377-0.08840.0236-0.19230.1301-0.494-0.32090.2356-0.02840.1518-0.036-0.02490.3-0.08730.37497.869744.329837.6282
20.7934-0.2187-0.14971.4236-0.15690.62820.0670.1910.0077-0.39820.2661-0.5825-0.58830.4864-0.13810.2258-0.12450.10290.3667-0.13150.37289.462849.805831.5826
31.1766-0.6272-0.14880.7792-0.32840.5980.09620.0037-0.31610.05020.0266-0.33010.16210.2286-0.07250.1544-0.0193-0.02610.2961-0.10450.40828.181137.26236.9608
40.6733-0.32160.00791.4775-0.61341.85540.1045-0.1143-0.3173-0.07720.0456-0.1470.27660.0685-0.02040.1340.0239-0.03910.2113-0.05430.3097-1.491434.084838.6141
51.1090.0838-0.58361.73140.11571.816-0.0238-0.06160.0132-0.08020.02020.07140.0087-0.3037-0.00390.1361-0.0207-0.03790.2385-0.05540.2363-6.872142.937738.3919
61.16920.27390.61181.38760.34591.53650.1097-0.03550.2639-0.00710.1312-0.0896-0.52390.139-0.19210.3035-0.04620.0280.2381-0.05050.2820.625856.567838.9274
72.4083-1.561-2.78231.21912.37494.57780.17850.04970.1683-0.0507-0.0873-0.02320.18360.14260.06180.7555-0.99750.03581.1267-0.27750.565819.137273.153621.1965
80.56780.7388-0.83493.969-0.24071.48490.00150.2330.5934-0.21830.2191-0.6366-0.01210.5702-0.01340.632-0.13950.17620.8492-0.16030.62116.647861.52814.1525
91.21531.11041.39863.6715-0.11752.3374-0.1257-0.1537-0.00890.1740.1450.46330.0082-0.13520.05720.3929-0.0540.12110.3375-0.07670.5225-1.777256.395212.1978
10-0.00630.08420.02180.0036-0.06450.05720.1923-0.0746-0.12270.01260.1747-0.1091-0.12440.2927-0.12531.0063-0.2117-0.14870.76090.02860.73372.351182.486650.1426
111.01650.25160.41990.67740.06681.47320.29990.06090.0111-0.0074-0.11080.2157-0.68420.665-0.06660.7009-0.30130.24740.3243-0.03960.45857.275368.153318.1249
122.04890.88320.10172.07420.86371.03370.254-0.00290.1115-0.4058-0.02050.1051-1.06080.4441-0.00280.7442-0.30180.24920.3803-0.06080.47517.498972.019114.3555
131.19280.1503-0.45831.43790.39461.4039-0.0432-0.2262-0.12940.76520.2638-0.68010.4940.5023-0.13990.18820.1983-0.26660.3901-0.08530.527110.03925.030352.9709
141.576-0.62770.67541.4109-0.37693.0350.03050.01720.05810.0201-0.01310.0532-0.1119-0.2585-0.01970.1664-0.0180.01890.2281-0.05510.1758-24.568350.609751.3041
151.4769-0.3997-0.81260.89650.40232.34920.09350.07850.1836-0.2220.1387-0.0251-0.7822-0.3725-0.12710.42030.19520.05350.35530.0690.2177-27.065456.77857.175
161.0256-0.84550.93151.0342-1.23672.13810.11930.1184-0.3195-0.11250.05130.13310.08650.1038-0.1310.20990.01360.00770.248-0.0790.3081-8.658517.354214.5626
171.06560.26611.15831.5185-0.1441.39370.0945-0.13320.21050.09740.10760.2394-0.1106-0.2059-0.02271.33921.0266-0.13341.03590.00030.9195-42.533674.881128.4219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 179 )
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 193 )
8X-RAY DIFFRACTION8chain 'A' and (resid 194 through 206 )
9X-RAY DIFFRACTION9chain 'A' and (resid 207 through 216 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 160 )
12X-RAY DIFFRACTION12chain 'B' and (resid 161 through 200 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 248 )
14X-RAY DIFFRACTION14chain 'C' and (resid 249 through 540 )
15X-RAY DIFFRACTION15chain 'C' and (resid 541 through 808 )
16X-RAY DIFFRACTION16chain 'C' and (resid 809 through 1052 )
17X-RAY DIFFRACTION17chain 'D' and (resid 457 through 468 )

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