[English] 日本語
Yorodumi
- PDB-6x07: Nic96 from S. cerevisiae bound by VHH-SAN12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x07
TitleNic96 from S. cerevisiae bound by VHH-SAN12
Components
  • Nucleoporin NIC96
  • VHH-SAN12
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / nanobody
Function / homology
Function and homology information


nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport ...nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / ribosomal large subunit export from nucleus / nuclear pore / protein import into nucleus / nuclear envelope / nuclear membrane
Similarity search - Function
Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAndersen, K. / 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 NIC96
B: VHH-SAN12


Theoretical massNumber of molelcules
Total (without water)91,0012
Polymers91,0012
Non-polymers00
Water2,306128
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)48.126, 79.653, 283.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Nucleoporin NIC96 / 96 kDa nucleoporin-interacting component / Nuclear pore protein NIC96


Mass: 76575.141 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: NIC96, YFR002W / Production host: Escherichia coli (E. coli) / References: UniProt: P34077
#2: Antibody VHH-SAN12


Mass: 14426.015 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 8,000 and 0.1M tri-sodium citrate pH 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 64457 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 44.39 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.038 / Net I/σ(I): 23.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6339 / CC1/2: 0.634 / Rpim(I) all: 0.677

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QX5

2qx5


Resolution: 2.1→60.91 Å / SU ML: 0.2745 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 1997 3.11 %
Rwork0.2271 62274 -
obs0.2277 64271 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 0 128 5770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115777
X-RAY DIFFRACTIONf_angle_d1.1017857
X-RAY DIFFRACTIONf_chiral_restr0.0735914
X-RAY DIFFRACTIONf_plane_restr0.00621011
X-RAY DIFFRACTIONf_dihedral_angle_d21.68992066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.35021400.35694367X-RAY DIFFRACTION99.51
2.16-2.210.34131410.32564409X-RAY DIFFRACTION99.82
2.21-2.280.37081400.3064414X-RAY DIFFRACTION99.78
2.28-2.350.31581400.29134353X-RAY DIFFRACTION99.76
2.35-2.440.31531420.28084433X-RAY DIFFRACTION99.8
2.44-2.530.28471430.27384443X-RAY DIFFRACTION99.96
2.53-2.650.25091420.25264432X-RAY DIFFRACTION99.89
2.65-2.790.32011420.26314406X-RAY DIFFRACTION99.93
2.79-2.960.28281430.24644453X-RAY DIFFRACTION99.96
2.96-3.190.26351450.25024500X-RAY DIFFRACTION99.94
3.19-3.510.22591420.23064453X-RAY DIFFRACTION99.98
3.51-4.020.22951470.20064561X-RAY DIFFRACTION99.98
4.02-5.070.20921450.17554532X-RAY DIFFRACTION99.72
5.07-60.910.20931450.21164518X-RAY DIFFRACTION93.8
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)
10.7930627179460.007991631388812.04660964676-1.12787130770.7320860220763.93666261006-0.531508395676-0.3441723785210.4136327454540.130361687968-0.1365687004410.184859204574-1.63435750128-0.4230148031050.6238438136971.68338475650.0356304421586-0.227718574280.78867522237-0.1248622509850.585786350027-15.550588457411.527377489763.2908749768
25.45641106123-0.9101160625430.425824066338.499306952761.01028473947.02187242874-0.233102991755-0.121474943603-0.1850201584540.2237430189470.06897017002230.7782243136020.425612249828-0.7662808443540.1978562574480.667167760536-0.04087437452960.01066812796980.435637799085-0.04906794231460.441741479155-26.3537324466-1.4399690624736.2929570069
31.56667858671-0.07865676372241.061212342871.24282135581.473122584275.32899845945-0.03455763209140.0351815323229-0.03603451854690.5058335886110.0293944564652-0.171599554169-0.04270818290.4641100106260.03452227467350.807090684617-0.0726975407141-0.04881476937050.452034664260.009797848287460.38384897531-11.531641596-7.1375877635540.5660641938
40.6347954690470.9029213297052.78065162710.04555715662082.45742517776.75213830574-0.1167947102420.0875132436592-0.0909384056042-0.4917567213880.1343212761740.0479917891001-0.212888374930.249591217358-0.05083318782141.09236566084-0.0647112146055-0.1781780280310.580055379312-0.0532883046190.4881236588370.03023130958847.7829417966586.8869823893
53.619354249820.2373628107041.384471750132.678103848560.6359029236514.913011414140.11271440519-0.183028559940.1108927584140.0473047545521-0.04354827864270.0726108528837-0.0216081784717-0.261941759554-0.04369674883150.162111946814-0.02114490482040.02284736362250.3337618296790.007410562609860.32087321192810.38506797120.4192631173132.885580723
64.32933072154-3.31932966951-1.191240155483.784759718950.6338394865626.024367907520.6181318527510.21290490845-0.810053394119-0.693734391936-0.23445603249-0.3290489009921.071359857810.635781383553-0.3997658664091.1080425452-0.0508332671905-0.2003099991350.447539959757-0.1044364336550.84457379191717.5031711011-10.1252540535118.459330563
71.62176966256-0.788006130311-0.694463615343.72301261469-0.4684182685740.4855599101250.444629737702-0.0444948085921-1.075624743120.780978299838-0.06841578955510.6017148609330.871819775991-0.102505227809-0.2452072942431.45417707981-0.18016759949-0.3374411422150.454068108826-0.02516332787691.000776332027.30981276899-16.2070932861121.448457009
86.15075428573-0.9927790452370.2847208280385.820857395450.7202632048123.574524858820.321797632115-0.715917489166-0.5633819213361.33760119719-0.036629810501-0.2462572565790.799471309132-0.110953128494-0.2052108630531.0413396461-0.147932112854-0.2155730814620.484020430993-0.003632068635930.50847030599410.4890479606-6.60454574306126.957449681
93.159324791080.729274934620.4001439238154.18905412681-0.8218965230331.295631822710.834420761340.243965383995-0.369061841858-0.04228443414310.0369115546059-0.4102723583411.021732649540.552861464189-0.7511077150590.9505438596810.00542174817718-0.223582496590.396527644665-0.07677523371740.84839841034519.4079414482-5.80291162996121.557917158
102.31766399965-0.3159399495721.140136944774.403171865390.1039584789021.2043179762-0.0523610467138-0.141526236498-0.5969277733040.8214633005730.3204171111690.1591015933961.08318769011-0.841509116686-0.3156425878142.00074929309-0.144654866159-0.4245848136130.479654758080.2001239643350.93973542262913.6071001273-19.7648906835132.774307376
113.66691424648-1.19362975852-0.5644400575434.92879114303-1.465155729033.83132467630.352878721956-0.347542919788-1.124796296440.5422537203440.021766116375-0.5963609990060.7226761619670.0834810186885-0.431370325021.33559143815-0.054187368815-0.1798920011390.469158064586-0.06464483984090.85639147670711.1269029909-14.1201241534118.69227978
128.01094132903-2.486384893573.672840929036.29700353176-5.17811916165.434092494960.378554892510.684116343053-1.75822226247-1.86475829669-0.03343919137680.4133251979940.247630499553-1.08962356435-0.2641470408590.936163190424-0.126531982397-0.2773329121840.696164929155-0.1346436893430.7508846123310.917847822697-7.92134285886117.205754202
137.87963954484-0.648739620933-1.602222652523.089607484950.01996084565634.28049710643-0.3992786830340.359380666431-1.04028987792-0.2100818819270.21127049122-0.1894071691811.096587175550.1206919062770.3403091077781.78563606298-0.0329622113399-0.2832879354630.467485456571-0.1037926149110.80138324432712.8868073059-19.2215533459119.238442797
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 199 through 312 )AA199 - 3121 - 105
22chain 'A' and (resid 313 through 383 )AA313 - 383106 - 176
33chain 'A' and (resid 384 through 469 )AA384 - 469177 - 262
44chain 'A' and (resid 470 through 667 )AA470 - 667263 - 444
55chain 'A' and (resid 668 through 839 )AA668 - 839445 - 617
66chain 'B' and (resid 2 through 33 )BB2 - 331 - 32
77chain 'B' and (resid 34 through 44 )BB34 - 4433 - 43
88chain 'B' and (resid 45 through 72 )BB45 - 7244 - 71
99chain 'B' and (resid 73 through 82 )BB73 - 8272 - 81
1010chain 'B' and (resid 83 through 90 )BB83 - 9082 - 89
1111chain 'B' and (resid 91 through 97 )BB91 - 9790 - 96
1212chain 'B' and (resid 98 through 104 )BB98 - 10497 - 103
1313chain 'B' and (resid 105 through 118 )BB105 - 118104 - 117

+
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