[English] 日本語
Yorodumi
- PDB-6x06: Nup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x06
TitleNup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11
Components
  • Nucleoporin NUP120
  • VHH-SAN11
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / nanobody
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore ...mRNA export from nucleus in response to heat stress / nuclear pore localization / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / mRNA export from nucleus / nuclear pore / protein export from nucleus / protein import into nucleus / double-strand break repair / nuclear envelope / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding
Similarity search - Function
Nucleoporin Nup120/160 / Nucleoporin Nup120/160
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.27 Å
AuthorsKnockenhauer, K.E. / Nordeen, S.A. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077537 United States
CitationJournal: Nat Commun / Year: 2020
Title: A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure.
Authors: Nordeen, S.A. / Andersen, K.R. / Knockenhauer, K.E. / Ingram, J.R. / Ploegh, H.L. / Schwartz, T.U.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoporin NUP120
K: VHH-SAN11


Theoretical massNumber of molelcules
Total (without water)101,1212
Polymers101,1212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.170, 193.170, 78.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 87432.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP120, RAT2, YKL057C, YKL313, YKL314 / Production host: Escherichia coli (E. coli) / References: UniProt: P35729
#2: Antibody VHH-SAN11


Mass: 13688.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 19% PEG 8,000, 0.1M magnesium chloride, 0.1M Tris/HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.25→83.65 Å / Num. obs: 11664 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 196.87 Å2 / CC1/2: 0.938 / Rpim(I) all: 0.052 / Net I/σ(I): 18.7
Reflection shellResolution: 4.25→4.4 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 1141 / CC1/2: 0.524 / Rpim(I) all: 0.512

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HXR

3hxr


Resolution: 4.27→83.65 Å / SU ML: 0.8303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 48.547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3593 1154 9.91 %
Rwork0.3339 10487 -
obs0.3364 11641 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 240.98 Å2
Refinement stepCycle: LAST / Resolution: 4.27→83.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5650 0 0 0 5650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245763
X-RAY DIFFRACTIONf_angle_d0.60537850
X-RAY DIFFRACTIONf_chiral_restr0.0406924
X-RAY DIFFRACTIONf_plane_restr0.0041001
X-RAY DIFFRACTIONf_dihedral_angle_d14.84041964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.27-4.460.41731340.40421206X-RAY DIFFRACTION90.91
4.46-4.70.39621470.36631311X-RAY DIFFRACTION99.73
4.7-4.990.42851380.37781321X-RAY DIFFRACTION99.45
4.99-5.370.45951440.35861312X-RAY DIFFRACTION100
5.38-5.910.38991440.39231332X-RAY DIFFRACTION100
5.92-6.770.44541490.42641303X-RAY DIFFRACTION98.98
6.77-8.520.36321480.36241339X-RAY DIFFRACTION99.87
8.53-83.650.29681500.27121363X-RAY DIFFRACTION98.31
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)
14.538416538623.13785471519-0.5377508952851.347747648041.470546436858.00331310991-0.655553086494-0.1832198023920.505029496914-0.3193333346360.1553641585530.4365119580850.30428311028-1.373316211150.2354260726060.442722478879-0.1019259969850.0002612536898841.86193269063-0.1852282995181.074021722961.4225833968475.39632153862.29285336047
23.321759373111.667315852242.748207471370.864963959294-0.5600843842491.1117663341-0.351649039608-0.6052763269481.356292031910.6460648597520.255528379907-0.1075714828670.1023885321280.8193295488930.4099072237521.220254340740.1798592563480.07165547268932.21121807198-0.02582364155511.855562352835.592628339579.076816934-7.88586547317
33.42893979312-0.4241400245120.6908325823023.045352479473.684554493575.10045009077-0.359004938016-0.5081979881150.910355281516-1.420154661740.7856974606550.5969166112874.210142079890.228235845049-0.2671899453382.87395742304-0.7639607474820.09679050827031.891826774240.566571333372.1952742592325.76061397355.6661549119-56.7473845804
46.702218128021.898962565243.031186332752.131164606252.992773198224.11539272169-2.10091606049-1.883830558592.198077802660.835534973412.107483585311.30656534467-2.712996174250.8841434137990.1386668528441.87639047031-0.25545991579-0.8620565762611.988511038070.812486119432.7455048446123.307712875665.5535703074-49.7394353303
55.555574040542.22626470066-0.7372021412163.603327740652.342862459294.8863750295-0.637935819962-1.346829269131.10821567956-2.361045248041.47277534053-0.322634315068-0.2293424666710.4128400063970.9838858251160.6041558673890.3705425006040.05200601036371.118380619080.5697880142922.6310005102619.9903553762.1254054152-43.45224015
62.16775182436-2.23418411431-2.33168443032.330747039192.41148279112.44732310928-0.0159273562567-1.83265138453-0.7765212409070.06378719210440.466091051064-0.4755407689150.8698142730831.32346328063-0.2294430494371.29375702692-0.503999650897-0.7122872264533.29181211751.311187624064.2878791504613.075688044455.2079899842-44.8617022097
70.929968677427-0.813056865247-0.5166623941373.64368313985-0.4246692416841.06098676861-1.7454284959-0.6635865031511.50347101065-2.716717770631.60403027018-1.42318284628-0.828265294580.05558551329290.2547921529361.07359237513-0.435529047736-0.233343195141.94762211946-0.08581160894191.7095527445220.987465096959.3665113438-49.1483099952
82.077222545283.9462216458-2.682988526869.60086080654-5.220732287815.65949817955-0.8726884445491.424520111111.08285802742-3.537944230590.5892965323571.188906425271.06594952056-1.62125878222-0.329795643974.280606443850.0221059124121-0.6317857434810.0872898523465-0.07987914354033.0350481509724.654432729666.4948804256-55.6785787219
95.06019529661.201980205771.007627373371.43140659717-0.1775828262911.201184801261.61587400894-0.929620943584-1.412326903610.672623509254-0.372118924854-1.002067607170.6268892215150.2643597274351.636171337282.5533782306-1.133661235510.2382621583011.69331127099-0.9614354968890.97870611675812.613672869551.2335165763-65.3148823685
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 392 )AA1 - 3921 - 311
22chain 'A' and (resid 393 through 714 )AA393 - 714312 - 615
33chain 'K' and (resid 1 through 24 )KB1 - 241 - 24
44chain 'K' and (resid 25 through 44 )KB25 - 4425 - 44
55chain 'K' and (resid 45 through 57 )KB45 - 5745 - 54
66chain 'K' and (resid 58 through 67 )KB58 - 6755 - 64
77chain 'K' and (resid 68 through 110 )KB68 - 11065 - 107
88chain 'K' and (resid 111 through 120 )KB111 - 120108 - 117
99chain 'K' and (resid 121 through 126 )KB121 - 124118 - 121

+
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