[English] 日本語
Yorodumi
- PDB-9i8a: NXT1-NXF1 complex crystallized in space group P65 2 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i8a
TitleNXT1-NXF1 complex crystallized in space group P65 2 2
Components
  • NTF2-related export protein 1
  • Nuclear RNA export factor 1
KeywordsTRANSPORT PROTEIN / Cancer Nuclear Transport Factor 2 Like Export Factor 1
Function / homology
Function and homology information


nuclear RNA export factor complex / nuclear pore central transport channel / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus ...nuclear RNA export factor complex / nuclear pore central transport channel / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / protein export from nucleus / small GTPase binding / cytoplasmic stress granule / protein transport / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / Nuclear transport factor 2/Mtr2 / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain ...Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / Nuclear transport factor 2/Mtr2 / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / RNA-binding domain superfamily / Leucine-rich repeat domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Nuclear RNA export factor 1 / NTF2-related export protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsKoekemoer, L. / Fairhead, M. / Wright, N.D. / Bowesman-Jones, H.J. / Adams, C.J. / Von Delft, F.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Cancer Research UKCGCATF-2023/100049 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)1OT2CA297644-01 United States
CitationJournal: To Be Published
Title: NXT1-NXF1 complex crystallized in space group P65 2 2
Authors: Koekemoer, L. / Fairhead, M. / Wright, N.D. / Bowesman-Jones, H.J. / Adams, C.J. / Von Delft, F.
History
DepositionFeb 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Nuclear RNA export factor 1
A: NTF2-related export protein 1


Theoretical massNumber of molelcules
Total (without water)36,8212
Polymers36,8212
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.332, 105.332, 171.409
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Nuclear RNA export factor 1 / Tip-associated protein / Tip-associating protein / mRNA export factor TAP


Mass: 21163.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NXF1, TAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU9
#2: Protein NTF2-related export protein 1 / Protein p15


Mass: 15657.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NXT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKK6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 3 M Sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.922 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 1.5→91.22 Å / Num. obs: 89974 / % possible obs: 100 % / Redundancy: 37.5 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 16.6
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 5.265 / Num. unique obs: 4422

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
xia2data reduction
xia2data scaling
SIMBADphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.501→91.22 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.167 / WRfactor Rwork: 0.157 / SU B: 7.506 / SU ML: 0.101 / Average fsc free: 0.9586 / Average fsc work: 0.9709 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2005 2020 2.247 %
Rwork0.1703 87859 -
all0.171 --
obs-89879 99.951 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.107 Å20.054 Å20 Å2
2--0.107 Å2-0 Å2
3----0.347 Å2
Refinement stepCycle: LAST / Resolution: 1.501→91.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 195 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122618
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162438
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.8063556
X-RAY DIFFRACTIONr_angle_other_deg0.6151.755606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.115517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84910432
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.74510123
X-RAY DIFFRACTIONr_chiral_restr0.0930.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
X-RAY DIFFRACTIONr_nbd_refined0.2090.2437
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21952
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21238
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3520.29
X-RAY DIFFRACTIONr_nbd_other0.1520.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.28
X-RAY DIFFRACTIONr_mcbond_it11.6143.561297
X-RAY DIFFRACTIONr_mcbond_other11.5893.5591297
X-RAY DIFFRACTIONr_mcangle_it15.746.3991620
X-RAY DIFFRACTIONr_mcangle_other15.7426.4021621
X-RAY DIFFRACTIONr_scbond_it14.2734.0121321
X-RAY DIFFRACTIONr_scbond_other14.2524.0111321
X-RAY DIFFRACTIONr_scangle_it19.9197.1831935
X-RAY DIFFRACTIONr_scangle_other19.9147.1851936
X-RAY DIFFRACTIONr_lrange_it23.74434.92797
X-RAY DIFFRACTIONr_lrange_other23.2633.9412757
X-RAY DIFFRACTIONr_rigid_bond_restr5.08135056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.501-1.540.3941620.34563440.34765320.890.9199.6020.394
1.54-1.5820.3831450.31662190.31863640.9030.9231000.369
1.582-1.6280.2891370.28160680.28162050.930.9471000.348
1.628-1.6780.2761340.2659330.26160670.9580.9561000.312
1.678-1.7330.2651260.2257260.22158520.9520.9711000.27
1.733-1.7930.2221120.19755480.19756600.970.9771000.239
1.793-1.8610.2531240.16653610.16854850.9620.9841000.2
1.861-1.9370.1971220.14551820.14653040.9820.9881000.169
1.937-2.0230.1871260.13449450.13550720.980.99199.98030.153
2.023-2.1220.1751140.13147560.13248700.9870.9921000.143
2.122-2.2370.175990.12945350.1346340.9850.9921000.138
2.237-2.3720.206920.12842960.1343880.9760.9921000.131
2.372-2.5360.22870.14440760.14541630.9710.9891000.138
2.536-2.7390.266940.16237700.16438640.9620.9861000.151
2.739-30.2910.17635070.17735980.9730.9821000.163
3-3.3540.198700.16831940.16932640.9710.9861000.158
3.354-3.8710.118700.13528410.13529110.9930.9911000.13
3.871-4.7390.122530.11424430.11424960.9890.9931000.113
4.739-6.6930.175390.1819420.1819810.9910.9891000.177
6.693-91.220.184230.25211730.25111960.9810.9531000.235

+
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