SAXSdb — 6x03

▼

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

Nucleoporin NUP84

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 4	Nucleoporin NUP133 × 1 （P36161） VHH-SAN8 × 1 VHH-SAN9 × 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–726； UniProt 1–726

Nucleoporin NUP133

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P36161

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nucleoporin NUP84 × 1 （P52891） VHH-SAN8 × 1 VHH-SAN9 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU133_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–643； UniProt 521–1157

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6x03
Deposition date deposition_date	2020-05-15
Structure title title	Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9
Keywords keywords	STRUCTURAL PROTEIN, Nucleoporin, Nanobody; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6x03__assembly_1__model_1

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

Download this curve (.dat)

6x03__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6x03__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	62.15 Å
Rg (electron density)	63.43 Å
Total Rg	63.01 Å
Atom count	7091
Residues	1429
Excluded volume	114210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6x03__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nucleoporin NUP84
Molecular weight formula_weight	83718.9 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	7091

MELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIWIVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEEDHIFFKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKHSLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIENYLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIHSSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYISLLKLQGLYENIPIYATFLNESDCLEACSFILSSLEDPQVRKKQIETINFLRLPASNILRRTTQRVFDETEQEYSPSNEISISFDVNNIDMHLIYGVEWLIEGKLYVDAVHSIIALSRRFLLNGRVKALEQFMERNNIGEICKNYELEKIADNISKDENEDQFLEEITQYEHLIKGIREYEEWQKSVSLLSSESNIPTLIEKLQGFSKDTFELIKTFLVDLTSSNFADSADYEILYEIRALYTPFLLMELHKKLVEAAKLLKIPKFISEALAFTSLVANENDKIYLLFQSSGKLKEYLDLVARTATLSN

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 NUP133
Molecular weight formula_weight	75009.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADPGFSLDQESIEHDLKLTSEEIFHSNGKYIPPMLNTLGQHLSVRKEFFQNFLTFVAKNFNYKISPELKLDLIEKFEILNCCIKFNSIIRQSDVLNDIWEKTLSNYNLTQNEHLTTKTVVINSPDVFPVIFKQFLNHVVFVLFPSQNQNFKLNVTNLINLCFYDGILEEGEKTIRYELLELDPMEVDTSKLPWFINFDYLNCINQCFFDFTFACEEEGSLDSYKEGLLKIVKILYYQFNQFKIWINTQPVKSVNANDNFININNLYDDNHLDWNHVLCKVNLKEQCIQIAEFYKDLSGLVQTLQTLDQNDSTTVSLYETFFNEFPKEFSFTLFEYLIKHKKLNDLIFRFPQQHDVLIQFFQESAPKYGHVAWIQQILDGSYADAMNTLKNITVDDSKKGESLSECELHLNVAKLSSLLVEKDNLDINTLRKIQYNLDTIDAEKNISNKLKKGEVQICKRFKNGSIREVFNILVEELKSTTVVNLSDLVELYSMLDDEESLFIPLRLLSVDGNLLNFEVKKFLNALVWRRIVLLNASNEGDKLLQHIVKRVFDEELPKNNDFPLPSVDLLCDKSLLTPEYISETYGRFPIDQNAIREEIYEEISQVETLNSDNSLEIKLHSTIGSVAKEKNYTINYETNTVEY

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 3 Entity 3 polymer

Description description	VHH-SAN8
Molecular weight formula_weight	14150.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QLQLVETGGGLVQAGGSLRLSCVASGRTFTSYAMGWFRQAPGKEREFVAAISRLASGTDYADSVKGRFTISRNNDKNTVYLQMNNLIPEDTAVYYCAALQALRFSLPIAMATMKNGRADSWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	VHH-SAN9
Molecular weight formula_weight	13826.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

QVQLVESGGGSVQAGGSLRLSCAVSGGTLSTLAMGWFRQAPGQEREFVARIGWTNGDTGYADSVKGRFTISRDNVKNTVYLQMNNLKPEDTALYYCATRRPYGSTLYPPNTESAHDNWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

▶

Unit-cell length a length_a	72.252 Å
Unit-cell length b length_b	295.205 Å
Unit-cell length c length_c	295.609 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	orthorhombic

Resolution resolution	7.300 Å
Low-resolution limit resolution_low	147.800 Å
R factor r_factor	0.3365
R_work r_work	0.3352
R_free r_free	0.3534

Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9

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

Nucleoporin NUP84

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP133

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

6x03__assembly_1__model_1

6x03__assembly_1__model_1 | I(q)

6x03__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 (4)

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

7. Citations (1)

Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9

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

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 NUP133

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

6x03__assembly_1__model_1

6x03__assembly_1__model_1 | I(q)

6x03__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 (4)

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

7. Citations (1)