8tie

Double nuclear outer ring of Nup84-complexes from the yeast NPC

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP120

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nucleoporin NUP85 × 2 （P46673） NUP145 isoform 1 × 2 （A0A8H4C085） Protein transport protein SEC13 × 2 （Q04491） Nucleoporin Seh1 × 2 Nucleoporin NUP84 × 2 （P52891） NUP133 isoform 1 × 2 （A0A6V8RYD2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU120_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain a； PDBConstruct 1–1037； UniProt 1–1037 Author chain l； PDBConstruct 1–1037； UniProt 1–1037

Nucleoporin NUP85

OrganismNot specified

UniProt P46673

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nucleoporin NUP120 × 2 （P35729） NUP145 isoform 1 × 2 （A0A8H4C085） Protein transport protein SEC13 × 2 （Q04491） Nucleoporin Seh1 × 2 Nucleoporin NUP84 × 2 （P52891） NUP133 isoform 1 × 2 （A0A6V8RYD2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUP85_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain b； PDBConstruct 1–744； UniProt 1–744 Author chain m； PDBConstruct 1–744； UniProt 1–744

NUP145 isoform 1

OrganismNot specified

UniProt A0A8H4C085

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nucleoporin NUP120 × 2 （P35729） Nucleoporin NUP85 × 2 （P46673） Protein transport protein SEC13 × 2 （Q04491） Nucleoporin Seh1 × 2 Nucleoporin NUP84 × 2 （P52891） NUP133 isoform 1 × 2 （A0A6V8RYD2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8H4C085_YEASX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain c； PDBConstruct 1–1317； UniProt 1–1317 Author chain n； PDBConstruct 1–1317； UniProt 1–1317

Protein transport protein SEC13

OrganismNot specified

UniProt Q04491

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nucleoporin NUP120 × 2 （P35729） Nucleoporin NUP85 × 2 （P46673） NUP145 isoform 1 × 2 （A0A8H4C085） Nucleoporin Seh1 × 2 Nucleoporin NUP84 × 2 （P52891） NUP133 isoform 1 × 2 （A0A6V8RYD2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC13_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain d； PDBConstruct 1–297； UniProt 1–297 Author chain o； PDBConstruct 1–297； UniProt 1–297

Nucleoporin NUP84

OrganismNot specified

UniProt P52891

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nucleoporin NUP120 × 2 （P35729） Nucleoporin NUP85 × 2 （P46673） NUP145 isoform 1 × 2 （A0A8H4C085） Protein transport protein SEC13 × 2 （Q04491） Nucleoporin Seh1 × 2 NUP133 isoform 1 × 2 （A0A6V8RYD2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUP84_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain f； PDBConstruct 1–726； UniProt 1–726 Author chain q； PDBConstruct 1–726； UniProt 1–726

NUP133 isoform 1

OrganismNot specified

UniProt A0A6V8RYD2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nucleoporin NUP120 × 2 （P35729） Nucleoporin NUP85 × 2 （P46673） NUP145 isoform 1 × 2 （A0A8H4C085） Protein transport protein SEC13 × 2 （Q04491） Nucleoporin Seh1 × 2 Nucleoporin NUP84 × 2 （P52891）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6V8RYD2_YEASX
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain g； PDBConstruct 1–1157； UniProt 1–1157 Author chain r； PDBConstruct 1–1157； UniProt 1–1157

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tie
Deposition date deposition_date	2023-07-19
Last revision last_revision	2023-10-11
Structure title title	Double nuclear outer ring of Nup84-complexes from the yeast NPC
Keywords keywords	nuclear pore complex, nucleocytoplasmic transport, nucleoporin, membrane protein, translocase, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8tie__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8tie__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tie__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	0.00 Å
Rg (electron density)	149.00 Å
Total Rg	148.70 Å
Atom count	76621
Residues	9479
Excluded volume	1369900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tie__assembly_1__model_1`	tetradecameric （14）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Nucleoporin NUP120
Molecular weight formula_weight	120560.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,l
Atom count atom_count	76621

MACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPYGSEYSNCLLLSNSEYICYHFSSRSTLLTFYPLSDAYHGKTINIHLPNASMNQRYTLTIQEVEQQLLVNVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTVRVPHFLFYVSPQFSVVFLEDGGLLGLKKVDGVHYEPLLFNDNSYLKSLTRFFSRSSKSDYDSVISCKLFHERYLIVLTQNCHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLPLENGLFQMGTLLVDSSGILTYTFQNNIPTNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGTASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTKTGDVERGFCNLKSRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPYNHSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGELPDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDIPVVLNDLINNQMKPGIFWKKDFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLDLHYKQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSFFMTFFRSYIIENTSHKNIRFFLENVECPFYLRHNEVQEFMFAMTLFSCGNFDQSYEIFQLHDYPEAINDKLPTFLEDLKSENYHGDSIWKDLLCTFTVPYRHSAFYYQLSLLFDRNNSQEFALKCISKSAEYSLKEIQIEELQDFKEKQHIHYLNLLIHFRMFEEVLDVLRLGHECLSDTVRTNFLQLLLQEDIYSRDFFSTLLRLCNAHSDNGELYLRTVDIKIVDSILSQNLRSGDWECFKKLYCFRMLNKSERAAAEVLYQYILMQADLDVIRKRKCYLMVINVLSSFDSAYDQWILNGSKVVTLTDLRDELRGL

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP85
Molecular weight formula_weight	84972.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b,m

MTIDDSNRLLMDVDQFDFLDDGTAQLSNNKTDEEEQLYKRDPVSGAILVPMTVNDQPIEKNGDKMPLKFKLGPLSYQNMAFITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLGDDRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIGRVKDQDGRVNRFYELEESLTVLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKVFETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDSSSTFREWKNLVLKLSQAFGSSATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCGFLLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISGKIHSILPVMESLDSCTAAFTAMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDKELWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIYTTLGNQMLSAHNIIESIANFSRAGKYELVKSYSWLLFEASCMEGQKLDDPVLNAIVSKNSPAEDDVIIPQDILDCVVTNSMRQTLAPYAVLSQFYELRDREDWGQALRLLLLLIEFPYLPKHYLVLLVAKFLYPIFLLDDKKLMDEDSVATVIEVIETKWDDADEKSSNLYETIIEADKSLPSSMATLLKNLRKKLNFKLCQAFM

Entity 3 Entity 3 polymer

Description description	NUP145 isoform 1
Molecular weight formula_weight	145810.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c,n

MFNKSVNSGFTFGNQNTSTPTSTPAQPSSSLQFPQKSTGLFGNVNVNANTSTPSPSGGLFNANSNANSISQQPANNSLFGNKPAQPSGGLFGATNNTTSKSAGSLFGNNNATANSTGSTGLFSGSNNIASSTQNGGLFGNSNNNNITSTTQNGGLFGKPTTTPAGAGGLFGNSSSTNSTTGLFGSNNTQSSTGIFGQKPGASTTGGLFGNNGASFPRSGETTGTMSTNPYGINISNVPMAVADMPRSITSSLSDVNGKSDAEPKPIENRRTYSFSSSVSGNAPLPLASQSSLVSRLSTRLKATQKSTSPNEIFSPSYSKPWLNGAGSAPLVDDFFSSKMTSLAPNENSIFPQNGFNFLSSQRADLTELRKLKIDSNRSAAKKLKLLSGTPAITKKHMQDEQDSSENEPIANADSVTNIDRKENRDNNLDNTYLNGKEQSNNLNKQDGENTLQHEKSSSFGYWCSPSPEQLERLSLKQLAAVSNFVIGRRGYGCITFQHDVDLTAFTKSFREELFGKIVIFRSSKTVEVYPDEATKPMIGHGLNVPAIITLENVYPVDKKTKKPMKDTTKFAEFQVFDRKLRSMREMNYISYNPFGGTWTFKVNHFSIWGLVNEEDAEIDEDDLSKQEDGGEQPLRKVRTLAQSKPSDKEVILKTDGTFGTLSGKDDSIVEEKAYEPDLSDADFEGIEASPKLDVSKDWVEQLILAGSSLRSVFATSKEFDGPCQNEIDLLFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGVSIKRLPTELQRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSILFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNEIEQIFLYLLLNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNISKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKFSLPYDDPIGVIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAAQLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRLKIPSQLIFNAQALKDRYEGNYLSEVQNLLLGSSYDLAEMAIVTSLGPRLLLSNNPVQNNELKTLREILNEFPDSERDKWSVSINVFEVYLKLVLDNVETQETIDSLISGMKIFYDQYKHCREVAACCNVMSQEIVSKILEKNNPSIGDSKAKLLELPLGQPEKAYLRGEFAQDLMKCTYKI

Entity 4 Entity 4 polymer

Description description	Protein transport protein SEC13
Molecular weight formula_weight	33083.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d,o

MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Entity 5 Entity 5 polymer

Description description	Nucleoporin Seh1
Molecular weight formula_weight	34652.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e,p

MQPFDSGHDDLVHDVVYDFYGRHVATCSSDQHIKVFKLDKDTSNWELSDSWRAHDSSIVAIDWASPEYGRIIASASYDKTVKLWEEDPDQEECSGRRWNKLCTLNDSKGSLYSVKFAPAHLGLKLACLGNDGILRLYDALEPSDLRSWTLTSEMKVLSIPPANHLQSDFCLSWCPSRFSPEKLAVSALEQAIIYQRGKDGKLHVAAKLPGHKSLIRSISWAPSIGRWYQLIATGCKDGRIRIFKITEKNLQVELLSEHDDHNGEVWSVSWNLTGTILSSAGDDGKVRLWKATYSNEFKCMSVITAQQ

Entity 6 Entity 6 polymer

Description description	Nucleoporin NUP84
Molecular weight formula_weight	83718.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	f,q

MELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEEDHIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKHSLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIENYLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYISLLKLQGLYENIPIYATFLNESDCLEACSFILSSLEDPQVRKKQIETINFLRLPASNILRRTTQRVFDETEQEYSPSNEISISFDVNNIDMHLIYGVEWLIEGKLYVDAVHSIIALSRRFLLNGRVKALEQFMERNNIGEICKNYELEKIADNISKDENEDQFLEEITQYEHLIKGIREYEEWQKSVSLLSSESNIPTLIEKLQGFSKDTFELIKTFLVDLTSSNFADSADYEILYEIRALYTPFLLMELHKKLVEAAKLLKIPKFISEALAFTSLVANENDKIYLLFQSSGKLKEYLDLVARTATLSN

Entity 7 Entity 7 polymer

Description description	NUP133 isoform 1
Molecular weight formula_weight	133452.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	g,r

MSEKKVHLRLRKELSVPIAVVENESLAQLSYEEESQASLMDISMEQQQLRLHSHFDNSKVFTENNRYIVKTLQTDYSSGFSNDDELNGYIDMQIGYGLVNDHKKVYIWNIHSTQKDTPYITVPFRSDDNDEIAVAPRCILTFPATMDESPLALNPNDQDETGGLIIIKGSKAIYYEDINSINNLNFKLSEKFSHELELPINSSGGEKCDLMLNCEPAGIVLSTNMGRIFFITIRNSMGKPQLKLGKLLNKPFKLGIWSKIFNTNSSVVSLRNGPILGKGTRLVYITTNKGIFQTWQLSATNSHPTKLIDVNIYEAILESLQDLYPFAHGTLKIWDSHPLQDESSQLFLSSIYDSSCNETYYILSTIIFDSSSNSFTIFSTYRLNTFMESITDTKFKPKIFIPQMENANDTNEVTSILVMFPNAVVITQVNSKLDSSYSMRRKWEDIVSLRNDIDIIGSGYDSKSLYVLTKQMGVLQFFVKENEETNSKPEVGFVKSHVDQAVYFSKINANPIDFNLPPEISLDQESIEHDLKLTSEEIFHSNGKYIPPMLNTLGQHLSVRKEFFQNFLTFVAKNFNYKISPELKLDLIEKFEILNCCIKFNSIIRQSDVLNDIWEKTLSNYNLTQNEHLTTKTVVINSPDVFPVIFKQFLNHVVFVLFPSQNQNFKLNVTNLINLCFYDGILEEGEKTIRYELLELDPMEVDTSKLPWFINFDYLNCINQCFFDFTFACEEEGSLDSYKEGLLKIVKILYYQFNQFKIWINTQPVKSVNANDNFININNLYDDNHLDWNHVLCKVNLKEQCIQIAEFYKDLSGLVQTLQTLDQNDSTTVSLYETFFNEFPKEFSFTLFEYLIKHKKLNDLIFRFPQQHDVLIQFFQESAPKYGHVAWIQQILDGSYADAMNTLKNITVDDSKKGESLSECELHLNVAKLSSLLVEKDNLDINTLRKIQYNLDTIDAEKNISNKLKKGEVQICKRFKNGSIREVFNILVEELKSTTVVNLSDLVELYSMLDDEESLFIPLRLLSVDGNLLNFEVKKFLNALVWRRIVLLNASNEGDKLLQHIVKRVFDEELPKNNDFPLPSVDLLCDKSLLTPEYISETYGRFPIDQNAIREEIYEEISQVETLNSDNSLEIKLHSTIGSVAKEKNYTINYETNTVEY

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Resolution resolution	8.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	29655

Double nuclear outer ring of Nup84-complexes from the yeast NPC

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin NUP120

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nucleoporin NUP85

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NUP145 isoform 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein SEC13

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nucleoporin NUP84

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NUP133 isoform 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8tie__assembly_1__model_1

8tie__assembly_1__model_1 | I(q)

8tie__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

7. Citations (1)