4xmn

Structure of the yeast coat nucleoporin complex, space group P212121

Method: X-RAY DIFFRACTION

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

Protein transport protein SEC13

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Nucleoporin NUP145 × 1 （P49687） Nucleoporin NUP84 × 1 （P52891） Nucleoporin NUP120 × 1 （P35729） Nucleoporin NUP85 × 1 （P46673） Antibody 87 light chain × 1 Antibody 87 heavy chain × 1	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–297； UniProt 2–297

Nucleoporin NUP145

Saccharomyces cerevisiae

UniProt P49687

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP84 × 1 （P52891） Nucleoporin NUP120 × 1 （P35729） Nucleoporin NUP85 × 1 （P46673） Antibody 87 light chain × 1 Antibody 87 heavy chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU145_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 15–652； UniProt 680–1317

Nucleoporin NUP84

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P52891

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145 × 1 （P49687） Nucleoporin NUP120 × 1 （P35729） Nucleoporin NUP85 × 1 （P46673） Antibody 87 light chain × 1 Antibody 87 heavy chain × 1	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	3
Chains and sequence ranges	Author chain F； PDBConstruct 5–454； UniProt 2–451

Nucleoporin NUP120

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P35729

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145 × 1 （P49687） Nucleoporin NUP84 × 1 （P52891） Nucleoporin NUP85 × 1 （P46673） Antibody 87 light chain × 1 Antibody 87 heavy chain × 1	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	4
Chains and sequence ranges	Author chain E； PDBConstruct 9–1045； UniProt 1–1037

Nucleoporin NUP85

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P46673

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145 × 1 （P49687） Nucleoporin NUP84 × 1 （P52891） Nucleoporin NUP120 × 1 （P35729） Antibody 87 light chain × 1 Antibody 87 heavy chain × 1	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	5
Chains and sequence ranges	Author chain D； PDBConstruct 14–684； UniProt 73–743

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	4xmn
Deposition date deposition_date	2015-01-14
Structure title title	Structure of the yeast coat nucleoporin complex, space group P212121
Keywords keywords	STRUCTURAL PROTEIN, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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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.

4xmn__assembly_1__model_1

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

Download this curve (.dat)

4xmn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xmn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	94.03 Å
Rg (electron density)	97.23 Å
Total Rg	97.52 Å
Atom count	19816
Residues	2641
Excluded volume	350020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xmn__assembly_1__model_1`	heptameric （7）	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	Protein transport protein SEC13
Molecular weight formula_weight	33129.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	19816

MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP145
Molecular weight formula_weight	75087.7 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSDQPDADFEGIEASPKLDVSKDWVEQLILAGSSLRSVFATSKEFDGPCQNEIDLLFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGVSIKRLPTELQRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSILFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNEIEQIFLYLLLNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNISKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKFSLPYDDPIGVIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAAQLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRLKIPSQLIFNAQALKDRYEGNYLSEVQNLLLGSSYDLAEMAIVTSLGPRLLLSNNPVQNNELKTLREILNEFPDSERDKWSVSINVFEVYLKLVLDNVETQETIDSLISGMKIFYDQYKHCREVAACCNVMSQEIVSKILEKNNPSIGDSKAKLLELPLGQPEKAYLRGEFAQDLMKCTYKI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nucleoporin NUP84
Molecular weight formula_weight	52435.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GPHMELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEEDHIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKHSLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIENYLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYISLLKLQGLYENIPIYATFLNESDCLEACSFILSS

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Nucleoporin NUP120
Molecular weight formula_weight	121607.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MHHHHHHSMACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPYGSEYSNCLLLSNSEYICYHFSSRSTLLTFYPLSDAYHGKTINIHLPNASMNQRYTLTIQEVEQQLLVNVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTVRVPHFLFYVSPQFSVVFLEDGGLLGLKKVDGVHYEPLLFNDNSYLKSLTRFFSRSSKSDYDSVISCKLFHERYLIVLTQNCHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLPLENGLFQMGTLLVDSSGILTYTFQNNIPTNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGTASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTKTGDVERGFCNLKSRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPYNHSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGELPDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDIPVVLNDLINNQMKPGIFWKKDFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLDLHYKQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSFFMTFFRSYIIENTSHKNIRFFLENVECPFYLRHNEVQEFMFAMTLFSCGNFDQSYEIFQLHDYPEAINDKLPTFLEDLKSENYHGDSIWKDLLCTFTVPYRHSAFYYQLSLLFDRNNSQEFALKCISKSAEYSLKEIQIEELQDFKEKQHIHYLNLLIHFRMFEEVLDVLRLGHECLSDTVRTNFLQLLLQEDIYSRDFFSTLLRLCNAHSDNGELYLRTVDIKIVDSILSQNLRSGDWECFKKLYCFRMLNKSERAAAEVLYQYILMQADLDVIRKRKCYLMVINVLSSFDSAYDQWILNGSKVVTLTDLRDELRGL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Nucleoporin NUP85
Molecular weight formula_weight	79188.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGSSHHHHHHSDQPLSYQNMAFITAKDKYKLYPVRIPRLDTSKEFSAYVSGLFEIYRDLGDDRVFNVPTIGVVNSNFAKEHNATVNLAMEAILNELEVFIGRVKDQDGRVNRFYELEESLTVLNCLRTMYFILDGQDVEENRSEFIESLLNWINRSDGEPDEEYIEQVFSVKDSTAGKKVFETQYFWKLLNQLVLRGLLSQAIGCIERSDLLPYLSDTCAVSFDAVSDSIELLKQYPKDSSSTFREWKNLVLKLSQAFGSSATDISGELRDYIEDFLLVIGGNQRKILQYSRTWYESFCGFLLYYIPSLELSAEYLQMSLEANVVDITNDWEQPCVDIISGKIHSILPVMESLDSCTAAFTAMICEAKGLIENIFEGEKNSDDYSNEDNEMLEDLFSYRNGMASYMLNSFAFELCSLGDKELWPVAIGLIALSATGTRSAKKMVIAELLPHYPFVTNDDIEWMLSICVEWRLPEIAKEIYTTLGNQMLSAHNIIESIANFSRAGKYELVKSYSWLLFEASCMEGQKLDDPVLNAIVSKNSPAEDDVIIPQDILDCVVTNSMRQTLAPYAVLSQFYELRDREDWGQALRLLLLLIEFPYLPKHYLVLLVAKFLYPIFLLDDKKLMDEDSVATVIEVIETKWDDADEKSSNLYETIIEADKSLPSSMATLLKNLRKKLNFKLCQAFM

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Antibody 87 light chain
Molecular weight formula_weight	23461.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MASDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Antibody 87 heavy chain
Molecular weight formula_weight	28615.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MKKNIAFLLASMFVFSIATNAYAEISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSIHWVRQAPGKGLEWVASISSYYGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYETLYWPYQNSGMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTGGSHHHHHH

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	117.130 Å
Unit-cell length b length_b	179.950 Å
Unit-cell length c length_c	441.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	7.600 Å
Low-resolution limit resolution_low	49.606 Å
R factor r_factor	0.3212
R_work r_work	0.3183
R_free r_free	0.3473

Structure of the yeast coat nucleoporin complex, space group P212121

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

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 NUP145

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4xmn__assembly_1__model_1

4xmn__assembly_1__model_1 | I(q)

4xmn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

7. Citations (1)