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- PDB-5dha: Crystal Structure of CPEB4 NES Reverse Mutant Peptide in complex ... -

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Basic information

Entry
Database: PDB / ID: 5dha
TitleCrystal Structure of CPEB4 NES Reverse Mutant Peptide in complex with CRM1-Ran-RanBP1
Components
  • Engineered Nuclear Export Signal Peptide (CPEB4 NES reverse mutant)
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / Peptides / HEAT repeat / Nuclear Export signal / Exportin-1 / Nuclear Transport
Function / homology
Function and homology information


Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus ...Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA re-export from nucleus / RNA nuclear export complex / pre-miRNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear export signal receptor activity / snRNA import into nucleus / Regulation of HSF1-mediated heat shock response / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / tRNA export from nucleus / SUMOylation of SUMOylation proteins / importin-alpha family protein binding / protein localization to kinetochore / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / nuclear export / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of chromatin organization proteins / spindle pole body / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / NLS-bearing protein import into nucleus / MAPK6/MAPK4 signaling / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / U5 snRNA binding / viral process / mRNA export from nucleus / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / U1 snRNA binding / protein export from nucleus / centriole / GTPase activator activity / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / G protein activity / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / G1/S transition of mitotic cell cycle / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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 domain / Ran binding protein RanBP1-like / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.95 Å
AuthorsFung, H.Y. / Chook, Y.M.
Funding support Hong Kong, United States, 6items
OrganizationGrant numberCountry
Croucher FoundationStudent Scholarship Hong Kong
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352 United States
University of Texas SouthwesternEndowed Scholars Program United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award United States
CitationJournal: Elife / Year: 2015
Title: Structural determinants of nuclear export signal orientation in binding to exportin CRM1.
Authors: Fung, H.Y. / Fu, S.C. / Brautigam, C.A. / Chook, Y.M.
History
DepositionAug 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: Engineered Nuclear Export Signal Peptide (CPEB4 NES reverse mutant)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9819
Polymers163,1584
Non-polymers8235
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-56 kcal/mol
Surface area57580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.279, 106.279, 304.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 (E. coli) / Strain (production host): BL21(DE3) / 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 / Fragment: RanDB1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41920
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117458.781 Da / Num. of mol.: 1 / Mutation: V441D,D536G,T539C,V540E,K541Q,Y1022C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Engineered Nuclear Export Signal Peptide (CPEB4 NES reverse mutant)


Mass: 2418.728 Da / Num. of mol.: 1 / Fragment: Nuclear Export Signal
Source method: isolated from a genetically manipulated source
Details: Engineered mutant sequence of CPEPB4 NES / Source: (gene. exp.) Homo sapiens (human) / Gene: CPEB4 / Plasmid: pMal / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 13 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 53.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 17% PEG3350, 100mM Bis-Tris, 10mM 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: Feb 20, 2015
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 36157 / % possible obs: 94.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 52.32 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.049 / Rrim(I) all: 0.125 / Χ2: 0.913 / Net I/av σ(I): 13.296 / Net I/σ(I): 8.3 / Num. measured all: 222497
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-35.70.89317720.6040.4060.9860.77496
3-3.065.70.75418180.6930.3440.8330.77396.2
3.06-3.115.70.65217840.7630.2950.7190.78596.1
3.11-3.185.70.51318020.8180.2310.5650.82396.1
3.18-3.255.70.44217930.880.20.4880.83496
3.25-3.325.70.38218040.8780.1730.4220.89695.8
3.32-3.415.70.30917950.930.140.3410.88795.8
3.41-3.55.70.27717900.9260.1250.3050.97995.4
3.5-3.65.70.20918030.9630.0940.2310.89495.5
3.6-3.725.70.18417850.9620.0820.2021.10595.1
3.72-3.855.80.15317980.9770.0680.1680.99695.1
3.85-45.90.12917970.9840.0570.1411.0594.9
4-4.1960.10418040.9890.0450.1140.95994.6
4.19-4.4160.10217920.9880.0440.1121.26794.6
4.41-4.686.30.08818230.9910.0370.0961.2594.1
4.68-5.046.50.07818010.9930.0320.0851.07993.9
5.04-5.556.90.07718090.9940.030.0830.97893.6
5.55-6.357.30.06918210.9940.0270.0750.77692.8
6.35-87.70.05118350.9960.0190.0550.68192.2
8-507.30.03819310.9970.0150.0410.63189.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HB2

4hb2


Resolution: 2.95→47.529 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 1713 5 %Random selection
Rwork0.1806 32552 --
obs0.1836 34265 89.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.25 Å2 / Biso mean: 53.9591 Å2 / Biso min: 10.73 Å2
Refinement stepCycle: final / Resolution: 2.95→47.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10817 0 51 8 10876
Biso mean--41.78 23.25 -
Num. residues----1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311089
X-RAY DIFFRACTIONf_angle_d0.57814999
X-RAY DIFFRACTIONf_chiral_restr0.0241715
X-RAY DIFFRACTIONf_plane_restr0.0021897
X-RAY DIFFRACTIONf_dihedral_angle_d11.3164134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9368-3.02330.31381060.25222013211968
3.0233-3.12080.36851190.25852263238276
3.1208-3.23230.28791320.24012512264485
3.2323-3.36170.27741440.22552748289292
3.3617-3.51470.26461510.2142834298595
3.5147-3.69990.27381490.19852842299195
3.6999-3.93160.27751500.18812861301195
3.9316-4.2350.23671500.16382857300795
4.235-4.66090.20391510.14712873302495
4.6609-5.33450.1991520.14782873302594
5.3345-6.71790.25051510.18492879303093
6.7179-47.53560.18191580.14682997315591
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)
12.1632-0.00941.9084.01711.63438.8265-0.10710.38110.0286-0.15060.4274-0.6412-0.47970.5194-0.32170.1945-0.02590.06780.2473-0.05980.46127.155146.478234.2327
23.3575-0.77511.04252.72990.36335.42170.04840.5831-0.0106-0.01160.3057-0.66-0.73850.7523-0.34790.2832-0.09060.10750.3925-0.02020.572510.330449.616132.9676
33.5539-1.5892-0.73632.35291.23972.95210.2853-0.0801-0.71320.29780.0844-0.81430.64030.1225-0.39380.27780.0396-0.06460.43420.06490.743211.385334.605338.2861
40.2922-0.6836-1.39297.463-0.16798.8268-0.0065-0.0072-0.11020.0538-0.0313-0.27880.38040.20620.01040.07190.01350.04370.1843-0.01430.3689-0.70437.955340.1755
53.7676-1.3546-0.37864.857-3.02517.53660.09420.17530.307-0.08950.05330.1221-0.4229-1.0531-0.10360.17610.0437-0.00230.3103-0.03840.2363-8.356945.377634.861
68.48943.4076-0.48713.2224-1.73547.8673-0.1020.1991.26960.3530.03960.2953-1.7143-0.312-0.07560.50650.06650.0270.28540.00070.40882.375458.239743.8904
78.4282-1.0752-5.07680.8541-1.11397.8423-0.16871.4669-0.1776-0.3950.048-0.29670.2598-0.30960.12981.1939-0.6459-0.0491.1044-0.04480.483821.231872.106319.2022
80.96952.6803-1.02657.4748-2.62635.04550.0564-0.84541.1189-0.59730.2717-0.4737-0.21931.2564-0.24440.5712-0.20040.18060.7308-0.24660.55319.375158.73798.1021
98.0711-5.6876-7.22524.70465.22376.72831.3066-0.96560.4129-1.18090.6532-0.8231-2.90292.7414-1.93120.9861-0.53010.07860.5353-0.18220.83783.928180.629246.8078
107.85631.5288-0.85122.0089-0.85055.4972-0.1698-0.1810.06470.33840.14790.9518-1.08410.45060.00540.4702-0.14810.18270.33580.06420.42584.531268.20119.5279
114.63783.2215.08078.15011.79716.07520.47640.4698-0.7414-0.13740.0321-0.96190.3255-0.0625-0.340.73290.01630.25590.64120.11770.576511.401153.790214.6188
121.5545-1.1985-0.0161.1160.24762.0102-0.12570.12580.10660.04910.0372-0.0638-1.22750.75310.07520.7276-0.2890.1470.5628-0.01350.47357.794970.531518.6979
137.47445.76590.33668.0871.76931.8316-0.36540.35240.5603-0.29310.22880.3926-0.93080.61070.18040.6949-0.21960.07680.49480.04610.42377.913671.725414.568
142.35210.006-0.38181.32280.60341.41470.0546-0.1682-0.14650.60960.0844-0.81210.25690.2677-0.05520.41790.0822-0.2710.34490.0240.7617.532825.31854.1905
152.5798-1.01821.84662.7533-1.00474.43450.00920.1003-0.08960.04340.03910.0482-0.2138-0.2141-0.02780.2665-0.00390.010.2979-0.06420.18-24.647151.006452.6618
160.9167-0.26780.20781.98141.37466.02530.30340.04490.2817-0.2104-0.06420.0151-0.8594-0.636-0.1810.57660.22390.11640.49430.11230.3402-35.515465.166920.161
174.0071-2.664-0.25734.17450.37971.4630.01610.2630.0575-0.33160.1903-0.0004-0.2626-0.0172-0.19740.3445-0.00740.05280.43280.0070.1484-18.606446.199-2.1216
181.501-1.1051.02492.1568-2.00312.82360.16260.1426-0.4328-0.16330.00490.30820.21090.015-0.15920.23790.01090.02950.3296-0.1180.4595-7.728614.6417.2377
193.24790.40663.06236.9691.36243.02740.21580.06950.4685-1.1813-0.53361.5331-0.6905-0.1880.3830.79930.43020.21660.79120.05420.7914-40.503675.941528.873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 31 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 66 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 84 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 122 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 158 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 179 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 193 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 194 through 216 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 65 through 82 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 97 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 98 through 106 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 160 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 200 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 268 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 269 through 520 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 521 through 669 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 670 through 844 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 845 through 1052 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 18 )D0

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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