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- PDB-6x07: Nic96 from S. cerevisiae bound by VHH-SAN12 -

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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 / nuclear pore nuclear basket / structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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