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- PDB-5uws: Crystal Structure of X11L2 NES Peptide in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 5uws
TitleCrystal Structure of X11L2 NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Amyloid beta A4 precursor protein-binding family A member 3
  • Exportin-1,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


MAPK6/MAPK4 signaling / RNA nuclear export complex / pre-miRNA export from nucleus / negative regulation of catalytic activity / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding ...MAPK6/MAPK4 signaling / RNA nuclear export complex / pre-miRNA export from nucleus / negative regulation of catalytic activity / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / spindle pole body / protein localization to kinetochore / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / enzyme inhibitor activity / nuclear export / Nuclear import of Rev protein / Neurexins and neuroligins / RNA export from nucleus / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / 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 / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / nuclear pore / U1 snRNA binding / centriole / protein export from nucleus / 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 / kinetochore / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / protein transport / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / amyloid-beta binding / midbody / ubiquitin-dependent protein catabolic process / actin cytoskeleton organization / chemical synaptic transmission / regulation of gene expression / in utero embryonic development / dendritic spine / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / enzyme binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / 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 / Phosphotyrosine interaction domain (PTB/PID) / Ran binding protein RanBP1-like / Phosphotyrosine interaction domain (PID) profile. / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI 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 / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rab subfamily of small GTPases / PDZ superfamily / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Amyloid-beta A4 precursor protein-binding family A member 3 / 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 / Resolution: 2.401 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 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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,Exportin-1
D: Amyloid beta A4 precursor protein-binding family A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9009
Polymers163,0774
Non-polymers8235
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-54 kcal/mol
Surface area58100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.646, 106.646, 304.628
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,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 Amyloid beta A4 precursor protein-binding family A member 3


Mass: 2337.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: X11L2 / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O96018*PLUS

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Non-polymers , 4 types, 326 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
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: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 69614 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Net I/σ(I): 24.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3419 / CC1/2: 0.672 / Rpim(I) all: 0.605 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.401→47.694 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 2003 2.95 %
Rwork0.1884 --
obs0.1894 67965 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→47.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10925 0 18 321 11264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311289
X-RAY DIFFRACTIONf_angle_d0.47915291
X-RAY DIFFRACTIONf_dihedral_angle_d14.7796863
X-RAY DIFFRACTIONf_chiral_restr0.0371741
X-RAY DIFFRACTIONf_plane_restr0.0021946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4008-2.46090.28651030.25093397X-RAY DIFFRACTION71
2.4609-2.52740.29611390.24194561X-RAY DIFFRACTION96
2.5274-2.60180.27741430.24184740X-RAY DIFFRACTION99
2.6018-2.68570.28581430.22364726X-RAY DIFFRACTION100
2.6857-2.78170.26081460.21384764X-RAY DIFFRACTION100
2.7817-2.89310.26031450.21664765X-RAY DIFFRACTION100
2.8931-3.02470.26181430.2234772X-RAY DIFFRACTION100
3.0247-3.18420.24511450.21764780X-RAY DIFFRACTION100
3.1842-3.38360.24121470.24797X-RAY DIFFRACTION100
3.3836-3.64480.2761460.18854826X-RAY DIFFRACTION100
3.6448-4.01140.17391480.17174853X-RAY DIFFRACTION100
4.0114-4.59140.1861480.14844889X-RAY DIFFRACTION100
4.5914-5.78310.17951500.1584943X-RAY DIFFRACTION100
5.7831-47.70290.18161570.17215149X-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)
11.1616-0.63580.42041.23110.93653.2349-0.2190.0944-0.0135-0.08270.0869-0.459-0.14150.09350.10070.1875-0.06010.00830.3345-0.12980.45477.946144.414938.1372
20.2717-0.4952-0.11241.61570.08150.0701-0.12570.5126-0.1018-0.54750.0423-0.27-0.22740.2521-0.00270.2571-0.08140.14940.4797-0.1560.49057.260246.292125.3673
30.8016-0.38740.09384.14490.14780.23260.20310.3406-0.46930.1990.0669-0.4735-0.78270.4304-0.15850.1978-0.10920.06830.4453-0.18880.609811.724852.9638.3088
41.2659-0.5978-0.03410.7626-0.07950.7554-0.02210.2893-0.2211-0.01750.2277-0.80650.14610.2641-0.04650.17930.0293-0.06880.3912-0.17140.64578.042437.142637.5293
50.5295-0.7978-0.00961.907-1.20552.6134-0.04070.0177-0.1923-0.20650.0683-0.31860.2768-0.1230.01270.19750.0121-0.01970.3055-0.08120.3873-1.661434.075238.9776
62.65150.02820.22872.16650.77910.866-0.1262-0.3263-0.00130.32150.1285-0.03760.06880.0402-0.00530.22310.0352-0.0260.3036-0.0980.34521.443643.419644.1606
71.0520.2594-0.30561.488-0.48872.40660.00440.1802-0.0129-0.13760.05490.04410.1011-0.2812-0.04260.20850.0212-0.04070.353-0.06310.2696-8.228745.422134.7179
81.02880.40980.53932.33560.09591.21510.2353-0.00060.3930.13280.1094-0.1164-0.4966-0.0194-0.12340.3077-0.020.01670.3047-0.07040.33332.444658.360143.6442
93.8292-0.7434-4.58960.29240.92297.13010.07120.0863-0.11760.0273-0.0747-0.150.21050.04070.08790.9697-0.76830.13761.3085-0.31110.74221.066672.194719.1076
103.89632.3065-1.33942.7794-0.25210.67360.08690.10480.2326-0.00730.1902-0.4706-0.14150.3978-0.03920.7079-0.3470.21011.2108-0.34470.662117.236861.04444.664
113.54631.31421.14014.2525-0.52022.855-0.0641-0.1918-0.01890.31170.11680.38420.115-0.19340.03990.4886-0.15440.16990.488-0.09690.6302-1.570156.178912.1496
12-0.00970.0157-0.0006-0.0139-0.00520.00630.02370.01430.2439-0.16590.2076-0.1493-0.35260.175-0.22121.0535-0.14730.28660.7999-0.03080.91372.283982.622350.7707
131.24090.23320.36770.8216-0.00421.8196-0.0384-0.0079-0.00010.17770.0450.2753-0.63220.9330.08380.6081-0.29140.18970.5947-0.04930.47567.477267.97621.4679
141.50530.84510.28821.97130.84481.1872-0.02250.12210.0625-0.41660.09020.2101-1.16710.940.10430.7777-0.42780.17660.6572-0.0310.51088.044170.622712.4778
151.0878-0.1579-0.11452.11010.06941.0233-0.1633-0.1763-0.00731.19650.3005-1.07540.92540.2985-0.15720.06850.2662-0.46210.3315-0.12120.76049.734824.72353.2179
161.0309-0.60620.55471.2668-0.43762.09440.0095-0.02580.03180.07910.0425-0.0088-0.1812-0.2761-0.04880.24130.02220.00870.348-0.06630.1844-25.435652.665649.5271
171.388-0.8356-0.14381.43130.53391.98910.09630.15070.1048-0.21250.069-0.0355-0.592-0.282-0.14320.39010.0590.04750.33210.05410.2037-26.432355.90544.3357
180.7006-0.77890.79181.0061-1.40622.02010.17430.0951-0.3074-0.09960.070.25910.14440.0654-0.20970.24560.0186-0.00320.3274-0.08870.4145-8.901417.344114.9146
193.07690.5619-0.30932.5171-0.23372.2020.0313-0.12780.45060.0802-0.02810.0437-0.2584-0.2294-0.03560.85890.23310.06090.49630.00770.4919-38.074176.635628.05
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 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 122 )
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 158 )
8X-RAY DIFFRACTION8chain 'A' and (resid 159 through 179 )
9X-RAY DIFFRACTION9chain 'A' and (resid 180 through 193 )
10X-RAY DIFFRACTION10chain 'A' and (resid 194 through 206 )
11X-RAY DIFFRACTION11chain 'A' and (resid 207 through 216 )
12X-RAY DIFFRACTION12chain 'B' and (resid 63 through 82 )
13X-RAY DIFFRACTION13chain 'B' and (resid 83 through 139 )
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 201 )
15X-RAY DIFFRACTION15chain 'C' and (resid -1 through 245 )
16X-RAY DIFFRACTION16chain 'C' and (resid 246 through 569 )
17X-RAY DIFFRACTION17chain 'C' and (resid 570 through 808 )
18X-RAY DIFFRACTION18chain 'C' and (resid 809 through 1053 )
19X-RAY DIFFRACTION19chain 'D' and (resid 56 through 72 )

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