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- PDB-5uwu: Crystal Structure of SMAD4 NES Peptide in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 5uwu
TitleCrystal Structure of SMAD4 NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Mothers against decapentaplegic homolog 4
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / atrioventricular valve formation / somite rostral/caudal axis specification / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / atrioventricular valve formation / somite rostral/caudal axis specification / activin responsive factor complex / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / positive regulation of luteinizing hormone secretion / regulation of hair follicle development / sebaceous gland development / SMAD protein complex / formation of anatomical boundary / epithelial cell migration / RUNX2 regulates bone development / positive regulation of follicle-stimulating hormone secretion / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / neuron fate specification / epithelial to mesenchymal transition involved in endocardial cushion formation / filamin binding / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / response to transforming growth factor beta / secondary palate development / MAPK6/MAPK4 signaling / FOXO-mediated transcription of cell cycle genes / brainstem development / negative regulation of cardiac muscle hypertrophy / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / atrioventricular canal development / RNA nuclear export complex / cardiac conduction system development / nuclear export signal receptor activity / pre-miRNA export from nucleus / positive regulation of extracellular matrix assembly / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Germ layer formation at gastrulation / sulfate binding / Signaling by BMP / Formation of definitive endoderm / cellular response to BMP stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / activin receptor signaling pathway / outflow tract septum morphogenesis / Signaling by Activin / importin-alpha family protein binding / U4 snRNA binding / Signaling by NODAL / RNA export from nucleus / spindle pole body / protein localization to kinetochore / nuclear export / cardiac muscle hypertrophy in response to stress / SMAD protein signal transduction / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / gastrulation with mouth forming second / I-SMAD binding / Nuclear import of Rev protein / neural crest cell differentiation / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / endothelial cell activation / Cardiogenesis / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / RUNX3 regulates CDKN1A transcription / nuclear import signal receptor activity / DNA metabolic process / NLS-bearing protein import into nucleus / dynein intermediate chain binding / branching involved in ureteric bud morphogenesis / adrenal gland development / embryonic digit morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / seminiferous tubule development / ribosomal subunit export from nucleus / positive regulation of cardiac muscle cell apoptotic process / single fertilization / positive regulation of transforming growth factor beta receptor signaling pathway / spermatid development / TGF-beta receptor signaling activates SMADs / mitotic sister chromatid segregation / R-SMAD binding / uterus development / ribosomal small subunit export from nucleus / positive regulation of SMAD protein signal transduction / ribosomal large subunit export from nucleus / developmental growth / epithelial to mesenchymal transition
Similarity search - Function
MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain ...MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / 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 / SMAD-like domain superfamily / 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 / SMAD/FHA domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran / Mothers against decapentaplegic homolog 4
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
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352, RP150053 United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award United States
University of Texas SouthwesternEndowed 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 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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: Mothers against decapentaplegic homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,64710
Polymers162,7884
Non-polymers8586
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-66 kcal/mol
Surface area57760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.385, 106.385, 304.222
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-1551-

HOH

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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 Mothers against decapentaplegic homolog 4 /


Mass: 2049.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4 / Plasmid: pMAL-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13485*PLUS

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Non-polymers , 5 types, 549 molecules

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


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
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, 16 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: Jul 16, 2015
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: 84661 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Net I/σ(I): 22.9
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2 / Num. unique obs: 4176 / CC1/2: 0.662 / Rpim(I) all: 0.406 / % possible all: 100

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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→45.771 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.35
RfactorNum. reflection% reflection
Rfree0.2114 2000 2.4 %
Rwork0.181 --
obs0.1818 83492 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.24→45.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10851 0 52 543 11446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311336
X-RAY DIFFRACTIONf_angle_d0.57515380
X-RAY DIFFRACTIONf_dihedral_angle_d15.9076902
X-RAY DIFFRACTIONf_chiral_restr0.0391752
X-RAY DIFFRACTIONf_plane_restr0.0031961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2405-2.29650.24781180.23374810X-RAY DIFFRACTION83
2.2965-2.35860.25031390.22535661X-RAY DIFFRACTION97
2.3586-2.4280.25711430.21875819X-RAY DIFFRACTION100
2.428-2.50630.2691430.21095800X-RAY DIFFRACTION100
2.5063-2.59590.25261430.20145860X-RAY DIFFRACTION100
2.5959-2.69980.22511420.1965808X-RAY DIFFRACTION100
2.6998-2.82270.22361440.19085862X-RAY DIFFRACTION100
2.8227-2.97150.19651450.19085880X-RAY DIFFRACTION100
2.9715-3.15760.27251440.19475879X-RAY DIFFRACTION100
3.1576-3.40140.20341440.18535918X-RAY DIFFRACTION100
3.4014-3.74350.21341470.17265933X-RAY DIFFRACTION100
3.7435-4.28480.17851470.15275979X-RAY DIFFRACTION100
4.2848-5.39710.16481480.14496036X-RAY DIFFRACTION100
5.3971-45.78050.20211530.18246247X-RAY DIFFRACTION98
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)
11.662-0.12350.73780.33830.56412.9975-0.06030.05990.0304-0.1280.1134-0.3433-0.2090.23020.07110.1574-0.03450.01570.2647-0.12520.37258.041544.56937.8786
20.5151-0.7502-0.20481.49910.69141.18110.04190.4648-0.1105-0.55420.157-0.4008-0.24650.3359-0.1620.2834-0.09080.13210.3773-0.13710.35667.232946.551425.2075
30.8392-0.7315-0.0483.14450.42451.56410.09210.17460.1059-0.01210.1745-0.6408-0.42530.5262-0.20850.2604-0.11770.07930.3425-0.12280.497211.84153.083138.0876
41.4017-0.3239-0.05380.4943-0.29020.2210.09760.1126-0.33390.01880.0569-0.60590.12440.2119-0.01120.1677-0.0019-0.04470.3028-0.11920.52488.187637.292437.1771
50.8702-0.2466-0.01051.6614-0.82142.25520.04110.0531-0.3747-0.09160.0543-0.2070.27440.0731-0.03390.1430.0367-0.05150.2016-0.06430.3145-1.454134.176938.714
61.5280.1667-0.25471.9311-0.01741.6971-0.0853-0.00540.0061-0.17950.055-0.022-0.0867-0.3441-0.05350.19770.0159-0.01120.2025-0.03520.2745-5.176243.205134.4454
71.3793-0.0925-0.32663.0271-1.38993.09340.01520.1215-0.0491-0.16710.04050.07390.2998-0.1697-0.0810.1495-0.0014-0.02790.2437-0.07130.2152-8.953442.81342.482
81.12660.36140.40671.43390.30481.35170.03520.03350.3754-0.08070.0564-0.0491-0.62720.0563-0.11480.319-0.01630.03710.2365-0.05210.28640.715256.65639.0082
91.4878-0.4029-1.00071.04141.27282.1474-0.06650.4326-0.022-0.22540.2289-0.29570.0505-0.0063-0.0670.8652-0.5930.16381.1504-0.23250.752221.280372.731217.4416
103.02970.6034-0.23972.6335-0.51761.94950.03070.15630.2581-0.18910.3003-0.0925-0.25380.8193-0.15440.5269-0.23930.18390.7272-0.2460.55229.037259.39397.7491
110.0078-0.0186-0.05270.1650.43411.05860.0546-0.2580.0112-0.00960.1314-0.1547-0.5970.3326-0.07260.7146-0.16130.1730.5073-0.08090.5823.382274.531133.0884
122.67180.18081.07741.8086-1.17161.30820.15680.1534-0.53220.01440.1651-0.39050.30340.4297-0.1380.5444-0.09590.14050.5517-0.03810.55311.241354.452514.3259
130.86920.13690.16851.2491-0.4340.2888-0.1562-0.06940.02090.09490.12350.2159-0.61330.32490.11180.7954-0.28180.19150.4079-0.05440.45076.605573.282325.1636
141.11991.11450.05561.71540.50630.3371-0.01770.1006-0.0955-0.23250.1783-0.1037-0.77160.8293-0.01050.5663-0.26650.15230.5601-0.06050.446611.131567.829514.4098
150.82690.77380.25022.57410.56720.1399-0.12710.21590.2533-0.29410.07950.1875-0.86030.3501-0.04570.8216-0.29780.14560.40680.0050.49344.242173.999212.0564
160.6116-0.13140.21.53490.50480.79670.0029-0.1726-0.10.96290.2373-0.79290.52830.3662-0.0330.21480.1982-0.33680.3278-0.10080.59638.201225.476853.5808
171.3889-0.52520.61781.3167-0.4142.32770.01910.04630.080.06850.0182-0.0119-0.1869-0.2394-0.04850.19040.02070.02360.2625-0.05090.1336-26.303454.394648.3283
182.0191-0.8308-0.40151.21830.43671.66570.0105-0.03260.1693-0.13540.14690.0034-0.5074-0.2163-0.12580.3290.08380.05630.30410.05780.1688-26.458355.74614.3951
190.7073-0.61740.71020.9571-1.28912.00030.15290.0736-0.2739-0.1080.08420.20020.15320.0414-0.16330.22540.0088-0.00020.2421-0.07580.3205-8.855317.440914.6949
204.588-0.24820.40834.96710.03894.37250.02320.00860.18210.06180.05590.1663-0.1129-0.049-0.05451.04590.350.12880.5770.09940.8667-33.912277.455926.8898
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 132 )
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 148 )
8X-RAY DIFFRACTION8chain 'A' and (resid 149 through 179 )
9X-RAY DIFFRACTION9chain 'A' and (resid 180 through 193 )
10X-RAY DIFFRACTION10chain 'A' and (resid 194 through 216 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 97 )
12X-RAY DIFFRACTION12chain 'B' and (resid 98 through 106 )
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 133 )
14X-RAY DIFFRACTION14chain 'B' and (resid 134 through 171 )
15X-RAY DIFFRACTION15chain 'B' and (resid 172 through 200 )
16X-RAY DIFFRACTION16chain 'C' and (resid -1 through 268 )
17X-RAY DIFFRACTION17chain 'C' and (resid 269 through 569 )
18X-RAY DIFFRACTION18chain 'C' and (resid 570 through 808 )
19X-RAY DIFFRACTION19chain 'C' and (resid 809 through 1053 )
20X-RAY DIFFRACTION20chain 'D' and (resid 141 through 149 )

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