[English] 日本語
Yorodumi
- PDB-3nc1: Crystal structure of the CRM1-RanGTP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nc1
TitleCrystal structure of the CRM1-RanGTP complex
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
KeywordsGTP-binding protein/transport protein / protein transport / GTP-binding protein-transport protein complex
Function / homology
Function and homology information


Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / Heme signaling / HuR (ELAVL1) binds and stabilizes mRNA / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / annulate lamellae ...Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / Heme signaling / HuR (ELAVL1) binds and stabilizes mRNA / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RHO GTPases Activate Formins / Separation of Sister Chromatids / regulation of centrosome duplication / RNA nuclear export complex / MAPK6/MAPK4 signaling / pre-miRNA export from nucleus / 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 / regulation of protein export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / 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 / DNA metabolic process / dynein intermediate chain binding / regulation of protein catabolic process / mitotic sister chromatid segregation / protein localization to nucleus / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / mRNA export from nucleus / ribosomal subunit export from nucleus / nuclear pore / Cajal body / centriole / protein export from nucleus / viral process / 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 / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / nuclear membrane / DNA-binding transcription factor binding / ribonucleoprotein complex / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
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, 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 / 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 / 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 / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Exportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
AuthorsGuttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.
Authors: Guttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: GTP-binding nuclear protein Ran
A: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6534
Polymers144,1052
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-16 kcal/mol
Surface area51350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.802, 216.158, 123.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein GTP-binding nuclear protein Ran / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4 / Androgen receptor-associated protein 24


Mass: 20738.096 Da / Num. of mol.: 1 / Mutation: Q69L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARA24, OK/SW-cl.81, RAN, RAN (GeneID: 5901) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P62826
#2: Protein Exportin-1 / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123367.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crm1, Xpo1, Xpo1 (GeneID: 103573) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q6P5F9
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl, 12% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.35→37.37 Å / Num. all: 30619 / Num. obs: 28804 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.12 % / Biso Wilson estimate: 115.503 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.0399 / Net I/σ(I): 18.06
Reflection shellResolution: 3.35→3.45 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.4998 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 6713 / Num. unique all: 1682 / Num. unique obs: 1679 / Rsym value: 0.5521 / % possible all: 66.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRM1 and RANGTP molecules taken from PDB entry 3GJX

3gjx


Resolution: 3.35→36.521 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.757 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0.04 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1328 5.02 %RANDOM
Rwork0.219 ---
obs0.221 26438 86.47 %-
all-28804 --
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 93.229 Å2 / ksol: 0.271 e/Å3
Displacement parametersBiso max: 333.6 Å2 / Biso mean: 151.245 Å2 / Biso min: 69.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-8 Å
Luzzati sigma a0.53 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.35→36.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9716 0 33 0 9749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029958
X-RAY DIFFRACTIONf_angle_d0.52813490
X-RAY DIFFRACTIONf_chiral_restr0.0391535
X-RAY DIFFRACTIONf_plane_restr0.0021711
X-RAY DIFFRACTIONf_dihedral_angle_d13.4553708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.3920.42300.38164967962
3.392-3.4370.387420.39871876067
3.437-3.4840.455310.3769172266
3.484-3.5340.424220.35867069262
3.534-3.5870.374310.32758261354
3.587-3.6430.276350.31966970463
3.643-3.7020.364460.3251068111499
3.702-3.7660.423370.28867371064
3.766-3.8350.344460.29381586176
3.835-3.9080.316660.268951101791
3.908-3.9880.265450.25884488980
3.988-4.0740.261530.25191897186
4.074-4.1690.312600.234985104592
4.169-4.2730.314470.221994104194
4.273-4.3890.25570.2011014107195
4.389-4.5170.242600.1841022108297
4.517-4.6630.179350.1781079111497
4.663-4.8290.237580.1821047110598
4.829-5.0220.222470.1871065111299
5.022-5.250.264750.2051035111098
5.25-5.5260.264620.2091066112898
5.526-5.8710.298490.2161074112398
5.871-6.3220.286490.2191065111499
6.322-6.9540.306510.2141091114299
6.954-7.9510.241580.2031101115999
7.951-9.9840.206660.1431091115799
9.984-36.5230.141700.1681133120398
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)
11.6172-0.1774-0.23792.7173-1.49460.88030.2141-0.4404-0.3653-0.57620.02870.4488-0.1288-0.039-0.02461.085-0.14790.02081.5048-0.33420.7427-34.485872.6885-21.4425
21.57150.6513-1.33820.82390.02473.1729-0.18050.17771.3335-2.02570.3928-0.6475-1.70911.644-0.37892.42720.0848-0.20072.0582-0.3982.0839-1.276786.3294-45.3636
30.9261-0.72110.04612.6692-2.18262.1307-0.19290.25140.71720.1683-0.499-0.1557-0.21020.68720.19151.6301-0.28570.09741.5053-0.10260.9733-8.631376.9423-49.0647
40.82160.5188-0.0342.498-0.88571.64-0.46120.9238-0.2224-0.9377-0.08330.37730.7862-0.52750.35671.4706-0.10810.22781.2272-0.03960.8666-6.035863.3028-47.5371
53.6099-0.0729-0.77055.5998-2.47765.014-0.27260.4035-0.2695-0.075-0.0487-0.1057-0.0436-0.07180.36471.2053-0.24060.08971.21-0.24420.5368-15.725945.8183-36.9819
63.20870.30751.7573.98760.63362.9529-0.2743-0.1139-0.6950.09860.23660.06960.0623-0.16660.21171.1764-0.18740.16281.32510.04930.599-25.156633.2588-16.7017
73.49720.5962-2.01073.26872.84534.2738-0.28310.5823-0.5936-0.1520.517-0.31580.57240.8254-0.11621.5366-0.07410.07731.68310.06560.5763-21.035143.27487.3794
88.8097-0.2551-0.06821.89460.50642.4929-0.2044-0.261-1.15211.27650.30810.16370.0210.570.3471.2304-0.08320.30081.3511-0.02160.0999-21.508161.971816.1704
93.236-1.5711-0.83162.7996-0.27980.52111.27841.3078-0.9102-1.4516-0.37740.2345-1.3817-0.4354-0.24961.2933-0.07180.23271.4392-0.07270.6199-14.764968.77181.1196
100.0142-0.0963-0.09590.92650.69310.51450.04940.656-0.3527-1.21130.0085-0.1928-0.12510.7662-0.24171.1165-0.0024-0.07131.7194-0.02781.247-28.956854.464-10.5541
110.77-0.99640.03381.299-0.08360.0628-0.7342-1.2997-0.14281.51020.89310.6972-0.3607-0.5359-0.18821.608-0.2004-0.13752.1542-0.29350.711-12.632978.771810.235
122.0967-1.72981.77073.199-1.23561.47290.3169-0.74630.38940.0496-0.4021-0.74510.1052-0.38850.09041.6186-0.01720.15461.6963-0.42070.8173-15.438885.10521.1067
133.1747-0.25770.22812.1743-2.02681.8865-0.70770.30060.79010.07660.41470.2211-0.2248-0.16750.28811.8445-0.0603-0.00181.6604-0.77591.2708-19.316498.0888-4.9758
142.2899-0.69180.531.03060.63834.7465-0.23510.82860.2085-0.3811-0.1419-0.32640.54-0.01460.42541.5637-0.3782-0.02791.0157-0.15051.0639-20.3845102.0067-27.3983
152.92780.24480.47830.8756-0.16464.32620.5826-1.4667-0.0084-0.5844-0.50320.211.32411.6873-0.63281.7483-0.1299-0.08151.319-0.33931.1832-29.709897.0536-35.4796
161.95251.219-1.00330.8844-0.27680.79780.24050.17441.515-1.565-0.1707-0.08790.45490.78010.00351.701-0.0184-0.16831.6042-0.15141.3109-34.902697.2898-42.4099
172.4972-0.61511.23482.3209-0.60214.8126-0.3638-0.3926-0.15481.25440.53581.25031.7091-0.8035-0.3951.2646-0.1108-0.33040.7908-0.28560.8135-46.10383.1853-45.1905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain CC8 - 180
2X-RAY DIFFRACTION2chain A and resid 1028:1059A1028 - 1059
3X-RAY DIFFRACTION3chain A and resid 969:1027A969 - 1027
4X-RAY DIFFRACTION4chain A and resid 908:963A908 - 963
5X-RAY DIFFRACTION5chain A and resid 767:907A767 - 907
6X-RAY DIFFRACTION6chain A and resid 627:766A627 - 766
7X-RAY DIFFRACTION7chain A and resid 533:626A533 - 626
8X-RAY DIFFRACTION8chain A and resid 468:532A468 - 532
9X-RAY DIFFRACTION9chain A and resid 449:467A449 - 467
10X-RAY DIFFRACTION10chain A and resid 425:448A425 - 448
11X-RAY DIFFRACTION11chain A and resid 402:424A402 - 424
12X-RAY DIFFRACTION12chain A and resid 311:401A311 - 401
13X-RAY DIFFRACTION13chain A and resid 240:310A240 - 310
14X-RAY DIFFRACTION14chain A and resid 145:239A145 - 239
15X-RAY DIFFRACTION15chain A and resid 120:144A120 - 144
16X-RAY DIFFRACTION16chain A and resid 67:119A67 - 119
17X-RAY DIFFRACTION17chain A and resid 4:66A4 - 66

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more