SAXSdb — 3iko

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

Protein transport protein SEC13

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP145C × 1 （P49687） Nucleoporin NUP84 × 1 （P52891）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP145C × 1 （P49687） Nucleoporin NUP84 × 1 （P52891）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP145C × 1 （P49687） Nucleoporin NUP84 × 1 （P52891）	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 1–297； UniProt 1–297 Author chain D； PDBConstruct 1–297； UniProt 1–297 Author chain G； PDBConstruct 1–297； UniProt 1–297

Nucleoporin NUP145C

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 3	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP84 × 1 （P52891）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP84 × 1 （P52891）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP84 × 1 （P52891）	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 15–442； UniProt 731–1158 Author chain E； PDBConstruct 15–442； UniProt 731–1158 Author chain H； PDBConstruct 15–442； UniProt 731–1158

Nucleoporin NUP84

Saccharomyces cerevisiae

UniProt P52891

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145C × 1 （P49687）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145C × 1 （P49687）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Protein transport protein SEC13 × 1 （Q04491） Nucleoporin NUP145C × 1 （P49687）	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 C； PDBConstruct 1–460； UniProt 1–460 Author chain F； PDBConstruct 1–460； UniProt 1–460 Author chain I； PDBConstruct 1–460； UniProt 1–460

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	3iko
Deposition date deposition_date	2009-08-06
Structure title title	Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex
Keywords keywords	;NPC, TRANSPORT, WD REPEAT, AUTOCATALYTIC CLEAVAGE, MRNA TRANSPORT, NUCLEAR PORE COMPLEX, NUCLEUS, PHOSPHOPROTEIN, TRANSLOCATION, PROTEIN TRANSPORT, Coiled coil, Membrane, Hydrolase, RNA-binding, Cytoplasmic vesicle, Endoplasmic reticulum, ER-Golgi transport, NUCLEAR PROTEIN, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN, 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.

3iko__assembly_1__model_1

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

Download this curve (.dat)

3iko__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3iko__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.68 Å
Rg (electron density)	48.61 Å
Total Rg	48.42 Å
Atom count	9092
Residues	1127
Excluded volume	162240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3iko__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3iko__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3iko__assembly_3__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Protein transport protein SEC13
Molecular weight formula_weight	33083.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G
Atom count atom_count	27032

MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP145C
Molecular weight formula_weight	51013.9 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H

MGSSHHHHHHSQDPFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGVSIKRLPTELQRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSILFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNEIEQIFLYLLLNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNISKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKFSLPYDDPIGVIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAAQLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRLKIPSQLIFNAQALKDRYEGNYL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nucleoporin NUP84
Molecular weight formula_weight	52864.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I

MELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEEDHIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKHSLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIENYLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYISLLKLQGLYENIPIYATFLNESDCLEACSFILSSLEDPQVRKK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id	3ikoA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3ikoB03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	690 —

Domain ID domain_id	3ikoC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ikoD01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3ikoE01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3ikoE03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	690 —

Domain ID domain_id	3ikoF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ikoG01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3ikoH01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3ikoH03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	690 —

Domain ID domain_id	3ikoI02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	101.397 Å
Unit-cell length b length_b	194.050 Å
Unit-cell length c length_c	327.806 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	12

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

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2340
R_free r_free	0.2730

Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex

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

Nucleoporin NUP145C

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP84

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3iko__assembly_1__model_1

3iko__assembly_1__model_1 | I(q)

3iko__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 (3)

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

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)

Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex

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 NUP145C

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3iko__assembly_1__model_1

3iko__assembly_1__model_1 | I(q)

3iko__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 (3)

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

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)