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- PDB-6x08: Nup85-Seh1 from S. cerevisiae bound by VHH-SAN2 -

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Basic information

Entry
Database: PDB / ID: 6x08
TitleNup85-Seh1 from S. cerevisiae bound by VHH-SAN2
Components
  • Nucleoporin NUP85
  • Nucleoporin SEH1
  • VHH-SAN2
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / nanobody
Function / homology
Function and homology information


Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins ...Seh1-associated complex / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / vacuolar membrane / nucleocytoplasmic transport / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / mRNA export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein import into nucleus / nuclear envelope / protein transport / nuclear membrane / positive regulation of DNA-templated transcription
Similarity search - Function
Nucleoporin Nup85-like / Nup85 Nucleoporin / Sec13/Seh1 family / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nucleoporin NUP85 / Nucleoporin SEH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.19 Å
AuthorsNordeen, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin SEH1
B: Nucleoporin NUP85
K: VHH-SAN2


Theoretical massNumber of molelcules
Total (without water)117,6093
Polymers117,6093
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)233.992, 233.992, 139.424
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Nucleoporin SEH1 / Nuclear pore protein SEH1 / SEC13 homolog 1


Mass: 39469.047 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: SEH1, YGL100W / Production host: Escherichia coli (E. coli) / References: UniProt: P53011
#2: Protein Nucleoporin NUP85 / Nuclear pore protein NUP85


Mass: 64622.883 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: NUP85, RAT9, YJR042W, J1624 / Production host: Escherichia coli (E. coli) / References: UniProt: P46673
#3: Antibody VHH-SAN2


Mass: 13517.038 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)
Has protein modificationY

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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: 4.68 Å3/Da / Density % sol: 73.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1M ammonium sulfate, di-sodium succinate pH 5.5, and the addition of 4% 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 4.19→117 Å / Num. obs: 17026 / % possible obs: 100 % / Redundancy: 37.9 % / Biso Wilson estimate: 176.25 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.056 / Net I/σ(I): 19.1
Reflection shellResolution: 4.19→4.35 Å / Mean I/σ(I) obs: 1.32 / Num. unique obs: 1665 / CC1/2: 0.642 / Rpim(I) all: 0.665

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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: 3EWE

3ewe


Resolution: 4.19→117 Å / SU ML: 0.6691 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3465 1700 10 %
Rwork0.3109 15295 -
obs0.3131 16995 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 207.31 Å2
Refinement stepCycle: LAST / Resolution: 4.19→117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6827 0 0 0 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00656969
X-RAY DIFFRACTIONf_angle_d0.94889489
X-RAY DIFFRACTIONf_chiral_restr0.05991082
X-RAY DIFFRACTIONf_plane_restr0.00541221
X-RAY DIFFRACTIONf_dihedral_angle_d14.40282410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.19-4.320.38381380.38121240X-RAY DIFFRACTION99.14
4.32-4.460.45461380.37581232X-RAY DIFFRACTION99.85
4.46-4.610.41711380.35621257X-RAY DIFFRACTION100
4.61-4.80.34071400.34241253X-RAY DIFFRACTION100
4.8-5.020.34331380.32811238X-RAY DIFFRACTION100
5.02-5.280.32291400.30651261X-RAY DIFFRACTION100
5.28-5.610.37571410.33521265X-RAY DIFFRACTION100
5.61-6.050.33151410.35231278X-RAY DIFFRACTION99.93
6.05-6.650.39991410.35931270X-RAY DIFFRACTION99.86
6.66-7.620.40981430.34941280X-RAY DIFFRACTION100
7.62-9.60.31121460.26891315X-RAY DIFFRACTION100
9.6-1170.3171560.27051406X-RAY DIFFRACTION99.74
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)
12.060668449742.72132501429-0.684673541774.73930690699-2.268772219984.546895018310.4532109823880.0323180072759-0.727018012081-0.01129096164680.006819877046250.3531328012331.18387074511-1.370616924366.01870025438E-51.52304427568-0.249608608579-0.1087716274611.40154733489-0.05169344533061.3876176488664.3315870578-89.847015083926.6025972364
20.9455450875020.178088568179-0.5618094928410.8594364489891.627030558523.508026103230.600306330079-0.3139804717850.5757916261660.642021670267-0.4945455085710.336759909783-0.368406037297-1.059871570493.19648019704E-81.62125355591-0.438103769050.05019281005091.515312277860.07014972547541.8758799541164.7480565862-67.092865352623.5140179302
34.078129590671.752216041040.3423388186852.361406636330.4855520742253.985568331711.74928724298-0.7003878351141.63086217913-1.337872791520.263960587371-1.975529708860.757733843463-0.2285407724352.577705293952.73718443686-1.75616785723-0.1116437268681.79210591970.7562907235781.9973917469961.0551888814-71.3390059752-3.5521684451
41.042169197330.013954260842-0.5300364147750.307718090266-0.1639910698320.6765934976320.5770591744330.2402482505470.4162656344480.2509000933850.5760627604280.493687536413-0.41271139091-0.8771097864844.179654397454.418358164520.3891317964710.5013809117272.206271874611.070039803881.503077501849.26507863-71.6696878332-0.076086823247
51.4302292288-0.339805659273-0.08493384327280.228768039350.5465151203481.89317655772-0.7334830470880.278905515543-0.06259321825141.11618598695-1.102177573810.177518481018-0.096484080111-0.898737401713-1.455663152941.43653946857-0.826831574934-0.1156735625771.69956806365-0.3617300803183.6150783258154.4371049476-74.53475699478.69009169667
61.25984096172-0.3864747774130.1749190846880.6891818360940.1157451977031.419669833322.06648930778-1.17767165317-0.564218863539-1.79790452166-0.845874042861-1.05069431295-1.046902638930.1513889495720.2894595573541.86639612739-0.51567913881-0.01965151474191.13856992419-0.2054216552012.0152697231363.1144140856-78.92501017545.15376431407
73.637315825480.422373658159-0.2845992865684.151055159040.9954779281612.494329267810.72115862738-0.275414626792-1.82305540441-0.6744410274860.867166562818-1.666583208140.840803430826-1.033419769310.3223570823032.06074620917-0.7155403909710.2712038725441.372182524440.2666857419591.6977540887892.9026183306-59.90147591124.3726206755
84.08817852399-1.81585863877-0.9992212611412.90619421127-0.6035134599571.074993787170.965841547404-1.13429603850.8936336373930.5712643127960.28943794278-0.3406075900650.260295736836-1.480391063570.03934313056722.52331764023-0.924482839910.713041816581.888590500440.604450391071.4422261611794.7361801139-58.078652276-4.42161339907
92.67430535319-2.985149467-0.5641432434834.11016961248-0.8879415390993.01770459924-0.599205990306-0.5072768774190.1979561056660.370813906889-0.4541445065370.665642639964-2.31430075213-1.28785909287-0.1098814891682.14794953593-0.5400501724130.10503457541.438150862430.3244496905281.4112249162390.4611590971-49.4302383643-8.46960236485
100.141403358152-0.164660950672-0.1908796694710.341232380174-0.2343215743370.4822576923890.714301901824-0.0930696993361-0.4318499486841.1117573282-0.5805481230961.498803128871.88506556982-0.188922231665-2.30595483681E-71.57632489296-0.636940848966-0.4353196295481.4757849325-0.1304312264391.9428658823180.720928378-43.6121802126-29.6748524346
112.191851227133.07914681884-2.038994380214.97851335379-1.999144814243.04749670286-0.5014712975870.6887592111310.300734171073-1.938090694731.22195418190.348996447679-0.961791358229-1.060005166460.006125333703882.61402515491-0.180668870043-0.4093238824341.507107742950.3146583315321.6066165853491.531419742-32.6622525884-28.1519712163
121.17125413911-0.608487281273-1.409456873250.9835372723051.540505047592.21988186988-0.0215327447046-0.166572918785-0.5287525546250.9690159125590.570493628878-0.636500718071-0.849492167501-2.2213633290.04731062028771.86262068135-0.290938604210.2438986804511.04116189310.1106170825921.0686186658880.6863107303-38.6831508646-7.0071873168
132.384005072013.08506652144-1.362599761774.24098550083-3.058916652413.939006032240.0619458964258-0.6128319764780.0614263961281-1.061013300610.7283214073860.250687012664-0.358797035665-0.5040205756970.0004258772138451.83997414267-0.624553532286-0.4917949002671.471597883830.3846397963511.9016699598187.5701885791-65.68124652713.213055621
141.97043057374-2.889313612291.734822255214.71156629892-3.319317557122.340065873512.24026252711-1.94656711891-1.439065557861.99565477156-0.4377198715750.98103100324-0.714314094194-0.2853134560231.534840548252.283456292870.6614579206510.1649678369772.891738731730.5124781159680.22316218356987.4244455585-90.788692773218.9371470838
155.654914500516.05033006341-1.517103136478.1031462335-1.231074425460.466260953011-0.05951624392241.85839399077-3.526933980942.00364611073-1.92575967561-2.00134416411.74654141173-3.305087678180.05164388096892.798105653540.142130782492-0.5834140172324.092979580680.6119966036381.6578075899265.1754927471-17.7704511424-28.5743703416
16-0.038290425914-0.0762839900463-0.09984086907181.790386980710.1774624557970.158415970925-1.33599103383-2.42299993469-1.914947342762.969464799241.308190334931.170180306611.42506412512-1.02058857968-0.7567659063860.7786362829071.69439367288-0.891913275340.09071325847472.041813054352.0049457637764.7175208414-23.0185698715-25.1561235249
175.2801355788-1.96906144606-3.526614352143.39467983258-0.3904436488446.53973604834-1.213387272431.711758498751.963502142480.44727145813-1.88740438622-2.880190300391.57888028263-0.969529423632-7.183272185154.233628774121.75769608466-0.7912920432543.407559605130.7833587154113.9278564186167.5900144573-10.7569640748-27.2647641397
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 64 through 168 )AA64 - 16864 - 168
22chain 'A' and (resid 169 through 347 )AA169 - 347169 - 310
33chain 'B' and (resid 47 through 56 )BB47 - 561 - 10
44chain 'B' and (resid 57 through 61 )BB57 - 6111 - 15
55chain 'B' and (resid 62 through 70 )BB62 - 7016 - 24
66chain 'B' and (resid 71 through 95 )BB71 - 9525 - 49
77chain 'B' and (resid 96 through 138 )BB96 - 13850 - 85
88chain 'B' and (resid 139 through 164 )BB139 - 16486 - 111
99chain 'B' and (resid 165 through 213 )BB165 - 213112 - 160
1010chain 'B' and (resid 214 through 254 )BB214 - 254161 - 192
1111chain 'B' and (resid 255 through 367 )BB255 - 367193 - 305
1212chain 'B' and (resid 368 through 402 )BB368 - 402306 - 340
1313chain 'B' and (resid 403 through 531 )BB403 - 531341 - 450
1414chain 'B' and (resid 532 through 556 )BB532 - 556451 - 475
1515chain 'K' and (resid 1 through 51 )KC1 - 511 - 51
1616chain 'K' and (resid 52 through 101 )KC52 - 10152 - 101
1717chain 'K' and (resid 102 through 125 )KC102 - 125102 - 125

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