[English] 日本語
Yorodumi
- PDB-6xte: Human karyopherin RanBP5 (isoform-1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xte
TitleHuman karyopherin RanBP5 (isoform-1)
Components
  • Antipain
  • Importin-5
KeywordsTRANSLOCASE / human karyopherin / PA-PB1 sub-complex nuclear import / influenza polymerase assembly / host-pathogen interaction
Function / homology
Function and homology information


GTPase inhibitor activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal protein import into nucleus / nuclear import signal receptor activity / vRNP Assembly / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear pore / cellular response to amino acid stimulus / small GTPase binding ...GTPase inhibitor activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal protein import into nucleus / nuclear import signal receptor activity / vRNP Assembly / nuclear localization sequence binding / NLS-bearing protein import into nucleus / nuclear pore / cellular response to amino acid stimulus / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / nucleolus / RNA binding / membrane / nucleus / cytoplasm
Similarity search - Function
Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Importin beta family / TOG domain / TOG / HEAT repeat ...Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Importin beta family / TOG domain / TOG / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Antipain / NICKEL (II) ION / Importin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Actinomycetia (high G+C Gram-positive bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsSwale, C. / McCarthy, A.A. / Ruigrok, R.W.H. / Crepin, T.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0017 France
CitationJournal: J.Mol.Biol. / Year: 2020
Title: X-ray Structure of the Human Karyopherin RanBP5, an Essential Factor for Influenza Polymerase Nuclear Trafficking.
Authors: Swale, C. / Da Costa, B. / Sedano, L. / Garzoni, F. / McCarthy, A.A. / Berger, I. / Bieniossek, C. / Ruigrok, R.W.H. / Delmas, B. / Crepin, T.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_conn.ptnr1_auth_asym_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_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_end
Revision 2.1Jan 31, 2024Group: 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
A: Importin-5
C: Antipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4575
Polymers124,3042
Non-polymers1533
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-26 kcal/mol
Surface area47640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.091, 96.313, 156.979
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Importin-5 / / Imp5 / Importin subunit beta-3 / Karyopherin beta-3 / Ran-binding protein 5 / RanBP5


Mass: 123697.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CSO-893 corresponds to an oxydazed form of the Cys-893
Source: (gene. exp.) Homo sapiens (human) / Gene: IPO5, KPNB3, RANBP5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O00410
#2: Protein/peptide Antipain / /


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 606.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Actinomycetia (high G+C Gram-positive bacteria)
References: Antipain
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM tri-sodium citrate pH 4.5, 12 % PEG 6000, 100 mM ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→48 Å / Num. all: 181499 / Num. obs: 41396 / % possible obs: 70.3 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.046 / Net I/σ(I): 9.3
Reflection shellResolution: 2.27→2.54 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2070 / CC1/2: 0.68 / Rpim(I) all: 0.452 / % possible all: 14.5

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W3U

3w3u


Resolution: 2.27→78.49 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.892 / SU R Cruickshank DPI: 0.563 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.54 / SU Rfree Blow DPI: 0.299 / SU Rfree Cruickshank DPI: 0.305
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 2155 -RANDOM
Rwork0.1988 ---
obs0.2019 41396 67.1 %-
Displacement parametersBiso mean: 71.91 Å2
Baniso -1Baniso -2Baniso -3
1-8.6076 Å20 Å20 Å2
2---8.0098 Å20 Å2
3----0.5978 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.27→78.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8446 0 14 84 8544
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098645HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9711711HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3051SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1482HARMONIC5
X-RAY DIFFRACTIONt_it8645HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1131SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6847SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.34
LS refinement shellResolution: 2.27→2.45 Å
RfactorNum. reflection% reflection
Rfree0.2586 42 -
Rwork0.2322 --
obs0.2336 828 6.78 %
Refinement TLS params.

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)
10.22640.06190.39430.8459-0.34111.17570.04-0.07170.1846-0.07170.02660.04860.18460.0486-0.0666-0.0431-0.01020.0258-0.09420.0295-0.0609-8.55733.354969.86
22.0642-0.9840.40361.1987-0.1250.4133-0.29880.28970.07180.28970.2454-0.09390.0718-0.09390.05340.07520.0345-0.031-0.1441-0.0628-0.15196.033135.661661.8948
30.80940.3818-0.46671.0941-0.35310.9323-0.10220.0228-0.04410.02280.0418-0.0326-0.0441-0.03260.06040.0656-0.0135-0.0396-0.1845-0.0457-0.057937.004413.632341.8226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|20 - A|450 }
2X-RAY DIFFRACTION2{ A|451 - A|800 }
3X-RAY DIFFRACTION3{ A|801 - A|1115 }

+
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://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