[English] 日本語
Yorodumi
- PDB-3wyf: Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wyf
TitleCrystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex
Components
  • Exportin-1
  • Gsp1p
  • Ran-specific GTPase-activating protein 2
KeywordsGTP-BINDING PROTEIN/GTP-BINDING PROTEIN INHIBITOR / HEAT REPEAT / NUCLEAR EXPORT / GTP-BINDING PROTEIN-GTP-BINDING PROTEIN INHIBITOR complex
Function / homology
Function and homology information


: / small GTPase binding => GO:0031267 / nuclear export signal receptor activity / spindle pole body / protein localization to kinetochore / U4 snRNA binding / nuclear export / nuclear import signal receptor activity / MAPK6/MAPK4 signaling / ribosomal large subunit export from nucleus ...: / small GTPase binding => GO:0031267 / nuclear export signal receptor activity / spindle pole body / protein localization to kinetochore / U4 snRNA binding / nuclear export / nuclear import signal receptor activity / MAPK6/MAPK4 signaling / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / nuclear pore / U1 snRNA binding / protein export from nucleus / GTPase activator activity / kinetochore / small GTPase binding / perinuclear region of cytoplasm / 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 / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Armadillo-like helical / Alpha Horseshoe / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / Exportin-1 / Ran-specific GTPase-activating protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae AWRI796 (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKoyama, M. / Shirai, N. / Matsuura, Y.
CitationJournal: Cell Rep / Year: 2014
Title: Structural insights into how yrb2p accelerates the assembly of the xpo1p nuclear export complex
Authors: Koyama, M. / Shirai, N. / Matsuura, Y.
History
DepositionAug 26, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 8, 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 / 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_asym_id / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gsp1p
B: Ran-specific GTPase-activating protein 2
C: Exportin-1
D: Gsp1p
E: Ran-specific GTPase-activating protein 2
F: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,01710
Polymers342,9226
Non-polymers1,0954
Water15,997888
1
A: Gsp1p
B: Ran-specific GTPase-activating protein 2
C: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0095
Polymers171,4613
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-65 kcal/mol
Surface area57630 Å2
MethodPISA
2
D: Gsp1p
E: Ran-specific GTPase-activating protein 2
F: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0095
Polymers171,4613
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-58 kcal/mol
Surface area55310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 155.950, 149.820
Angle α, β, γ (deg.)90.00, 106.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein Gsp1p


Mass: 24825.357 Da / Num. of mol.: 2 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae AWRI796 (yeast)
Strain: AWRI796 / Gene: AWRI796_3356 / Plasmid: PGEX-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E7KFU1
#2: Protein Ran-specific GTPase-activating protein 2 / Ran-binding protein 2 / RANBP2


Mass: 26237.648 Da / Num. of mol.: 2 / Fragment: UNP residues 90-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: AWRI796_2363, YIL063C, YRB2 / Plasmid: PET30A-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40517
#3: Protein Exportin-1 / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 120398.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288C / Gene: CRM1, G8514, KAP124, XPO1, YGR218W / Plasmid: PET30A-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30822

-
Non-polymers , 3 types, 892 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M CITRATE, 17% PEG6000, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.776
11H, -K, -H-L20.224
ReflectionResolution: 2.22→33.69 Å / Num. obs: 187333 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 %
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 2.6 % / % possible all: 90.6

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M1I

3m1i


Resolution: 2.22→33.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.407 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.214 9474 5.1 %RANDOM
Rwork0.175 ---
obs0.177 177820 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.06 Å2
Baniso -1Baniso -2Baniso -3
1-12.4 Å20 Å213.46 Å2
2--0.99 Å20 Å2
3----13.39 Å2
Refinement stepCycle: LAST / Resolution: 2.22→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21466 0 66 888 22420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01921940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.96129737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64252681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35225.036985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.184153890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3771587
X-RAY DIFFRACTIONr_chiral_restr0.120.23460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 637 -
Rwork0.235 11706 -
obs--87.76 %

+
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