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- PDB-5uwi: Crystal Structure of HDAC5 NES Peptide in complex with CRM1-Ran-RanBP1 -

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Basic information

Entry
Database: PDB / ID: 5uwi
TitleCrystal Structure of HDAC5 NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Histone deacetylase 5
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


regulation of myotube differentiation / regulation of protein binding / negative regulation of myotube differentiation / 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 ...regulation of myotube differentiation / regulation of protein binding / negative regulation of myotube differentiation / 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 / negative regulation of cell migration involved in sprouting angiogenesis / protein localization to kinetochore / histone deacetylase / SUMOylation of RNA binding proteins / protein localization to nucleolus / U4 snRNA binding / Rev-mediated nuclear export of HIV RNA / spindle pole body / 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 / protein lysine deacetylase activity / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / histone deacetylase activity / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / MAPK6/MAPK4 signaling / B cell activation / mitotic sister chromatid segregation / histone deacetylase complex / ribosomal large subunit export from nucleus / U5 snRNA binding / viral process / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / U1 snRNA binding / ribosomal small subunit export from nucleus / centriole / B cell differentiation / GTPase activator activity / protein export from nucleus / positive regulation of DNA-binding transcription factor activity / protein kinase C binding / Regulation of PTEN gene transcription / mitotic spindle organization / transcription corepressor binding / response to activity / Transcriptional regulation by small RNAs / response to cocaine / recycling endosome / small GTPase binding / kinetochore / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / G1/S transition of mitotic cell cycle / histone deacetylase binding / positive regulation of protein import into nucleus / cellular response to insulin stimulus / neuron differentiation / protein import into nucleus / GDP binding / positive regulation of protein binding / nuclear envelope / melanosome / mitotic cell cycle / G protein activity / cellular response to lipopolysaccharide / midbody / ubiquitin-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear speck / cadherin binding / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / response to xenobiotic stimulus / cell division / negative regulation of DNA-templated transcription / GTPase activity / chromatin binding / GTP binding / chromatin / nucleolus
Similarity search - Function
Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / 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 ...Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / 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 / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Ureohydrolase domain superfamily / 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 / 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 / Histone deacetylase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 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
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 SouthwesternEndowed Scholars Program 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: Histone deacetylase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,39610
Polymers162,4814
Non-polymers9156
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-58 kcal/mol
Surface area57960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.391, 106.391, 304.723
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-1645-

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 / 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 Histone deacetylase 5


Mass: 1741.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC5 / Plasmid: pMAL-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UQL6*PLUS

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Non-polymers , 4 types, 741 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 53.5 %
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, 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: 2.14→50 Å / Num. obs: 95683 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.310682049 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Net I/σ(I): 26.4
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2 / Num. unique obs: 4777 / CC1/2: 0.679 / Rpim(I) all: 0.4 / % possible all: 99.7

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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: 2.143→40.29 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.11
RfactorNum. reflection% reflection
Rfree0.2184 2000 2.11 %
Rwork0.1827 --
obs0.1834 94939 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.143→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10945 0 24 735 11704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211340
X-RAY DIFFRACTIONf_angle_d0.53615368
X-RAY DIFFRACTIONf_dihedral_angle_d15.2226893
X-RAY DIFFRACTIONf_chiral_restr0.0381752
X-RAY DIFFRACTIONf_plane_restr0.0031956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1435-2.19710.32621290.25386014X-RAY DIFFRACTION91
2.1971-2.25650.26021400.2386488X-RAY DIFFRACTION97
2.2565-2.32290.2351430.2186629X-RAY DIFFRACTION99
2.3229-2.39780.25811420.2076635X-RAY DIFFRACTION100
2.3978-2.48350.26331430.19436657X-RAY DIFFRACTION100
2.4835-2.58290.21161440.1926667X-RAY DIFFRACTION99
2.5829-2.70050.22321430.18456657X-RAY DIFFRACTION99
2.7005-2.84280.19461440.18656670X-RAY DIFFRACTION99
2.8428-3.02090.26381440.18946694X-RAY DIFFRACTION99
3.0209-3.2540.22371430.18996675X-RAY DIFFRACTION99
3.254-3.58130.24211450.18056716X-RAY DIFFRACTION99
3.5813-4.09910.20021450.16126731X-RAY DIFFRACTION98
4.0991-5.16270.15921460.14436761X-RAY DIFFRACTION98
5.1627-40.29680.19911490.1796945X-RAY DIFFRACTION96
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)
10.03950.0447-0.02620.0473-0.02720.01410.05120.03540.0229-0.01130.0425-0.1313-0.12140.11260.12350.1451-0.11280.08380.254-0.13860.30949.147748.627232.9569
20.007-0.01230.00260.0285-0.01050.00440.0101-0.0197-0.0170.0309-0.0012-0.13110.00910.0659-0.02750.03570.0111-0.03760.2263-0.10520.34918.103237.192337.1475
30.03420.024-0.01930.0194-0.01350.01-0.02390.0285-0.0969-0.0123-0.0003-0.05090.02930.0055-0.07320.05890.0087-0.03510.1388-0.0720.2242-1.568934.068638.6985
40.01140.0059-0.01060.0239-0.00130.00870.03150.03030.0155-0.0443-0.0110.01450.0121-0.06510.02040.08860.0115-0.04280.1695-0.0530.1758-5.297143.09534.3638
50.00190.0005-0.00690.00630.0010.02210.0370.00970.006-0.00790.00790.01140.0295-0.04090.0040.07910.0083-0.03410.1966-0.06470.1633-9.107642.708742.5137
60.0101-0.00430.00160.0126-0.00640.00290.12230.02260.1274-0.0709-0.0011-0.0084-0.1105-0.00800.228-0.03610.03870.1786-0.05890.24140.59856.567738.9199
70.00540.00470.00240.00360.00270.00360.02180.00690.00530.0078-0.0122-0.01070.010.004900.6177-0.27830.13240.7933-0.11380.628419.667673.765820.255
80.00120.0005-0.00150.0006-0.00020.00350.01350.00160.0042-0.01340.0126-0.01090.011-0.010200.5209-0.16860.1280.6246-0.11990.501518.535462.70184.4811
90.00240.00060.00030.00240.00060.0013-0.00210.0043-0.00320.0010.0185-0.0001-0.00090.0029-00.3396-0.09410.12620.36-0.11260.484-1.643856.362712.1647
100.00840.0107-0.00140.0099-0.00050.00260.007-0.00030.0115-0.00820.00440.0201-0.00280.009200.7974-0.15030.04580.7595-0.02040.69022.611581.693149.5681
110.01630.00770.00460.0071-0.00460.0126-0.02260.02670.00990.05490.0018-0.0064-0.0880.067400.4453-0.13250.18720.3174-0.0360.46536.823163.182317.3802
120.01230.0037-0.00210.0158-0.00320.0019-0.0343-0.0071-0.0165-0.0121-0.00380.0153-0.06390.0383-0.05080.5616-0.23940.22430.2616-0.00060.46276.529173.187325.0504
130.00520.01470.01180.0550.04060.0287-0.01090.0092-0.0173-0.0714-0.00090.0057-0.23990.1973-0.00410.4993-0.26440.14160.3392-0.01480.45957.944470.553213.1966
140.05940.00940.02710.40740.20460.2061-0.012-0.2363-0.11130.47570.264-0.73870.18520.57870.6914-0.11250.2245-0.27640.2851-0.04640.459610.133224.736452.8357
150.3096-0.0447-0.10320.39390.18740.61390.050.02670.00310.02720.0224-0.0209-0.1519-0.22490.46210.12610.02120.01570.2259-0.03710.0973-25.255352.480749.3027
160.1519-0.028-0.24210.29120.12470.44450.0568-0.0960.1764-0.10480.18310.0523-0.412-0.33310.64050.50910.30750.11950.49170.12650.166-33.489762.75619.9087
170.1983-0.06130.09050.2625-0.07440.14380.03070.1552-0.0098-0.0950.0842-0.0098-0.1087-0.03150.42010.15540.02480.05730.2444-0.01970.117-15.744539.57490.7744
180.1743-0.00650.12420.3801-0.15740.17760.0747-0.0154-0.2748-0.1460.06340.15160.10330.02160.06340.12670.0215-0.01240.1648-0.05010.2842-6.925210.427120.5824
190.0011-0.00070.00020.0016-0.00020.0001-0.003-0.0109-0.0011-0.00580.01360.0022-0.0086-0.0125-00.76760.30730.14380.64530.03740.663-40.475774.506528.4898
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 111 )
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 132 )
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 179 )
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 190 )
8X-RAY DIFFRACTION8chain 'A' and (resid 191 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 106 )
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 133 )
13X-RAY DIFFRACTION13chain 'B' and (resid 134 through 200 )
14X-RAY DIFFRACTION14chain 'C' and (resid -1 through 245 )
15X-RAY DIFFRACTION15chain 'C' and (resid 246 through 569 )
16X-RAY DIFFRACTION16chain 'C' and (resid 570 through 692 )
17X-RAY DIFFRACTION17chain 'C' and (resid 693 through 897 )
18X-RAY DIFFRACTION18chain 'C' and (resid 898 through 1053 )
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 1095 )

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