SAXSdb — 3wyf

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

Gsp1p

Saccharomyces cerevisiae AWRI796

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ran-specific GTPase-activating protein 2 × 1 （P40517） Exportin-1 × 1 （P30822） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ran-specific GTPase-activating protein 2 × 1 （P40517） Exportin-1 × 1 （P30822） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E7KFU1_YEASA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 1–219 Author chain D； PDBConstruct 1–219； UniProt 1–219

Ran-specific GTPase-activating protein 2

Saccharomyces cerevisiae S288c

UniProt P40517

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Gsp1p × 1 （E7KFU1） Exportin-1 × 1 （P30822） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Gsp1p × 1 （E7KFU1） Exportin-1 × 1 （P30822） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YRB2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–238； UniProt 90–327 Author chain E； PDBConstruct 1–238； UniProt 90–327

Exportin-1

Saccharomyces cerevisiae S288c

UniProt P30822

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Gsp1p × 1 （E7KFU1） Ran-specific GTPase-activating protein 2 × 1 （P40517） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Gsp1p × 1 （E7KFU1） Ran-specific GTPase-activating protein 2 × 1 （P40517） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XPO1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–1049； UniProt 1–1084 Author chain F； PDBConstruct 3–1049； UniProt 1–1084

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	3wyf
Deposition date deposition_date	2014-08-26
Structure title title	Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex
Keywords keywords	HEAT REPEAT, NUCLEAR EXPORT, GTP-BINDING PROTEIN-GTP-BINDING PROTEIN INHIBITOR complex; GTP-BINDING PROTEIN/GTP-BINDING PROTEIN INHIBITOR
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.

3wyf__assembly_1__model_1

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

Download this curve (.dat)

3wyf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wyf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.27 Å
Rg (electron density)	35.34 Å
Total Rg	35.94 Å
Atom count	10920
Residues	1373
Excluded volume	196260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wyf__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wyf__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Gsp1p
Molecular weight formula_weight	24825.4 kDa
Mutation mutation	Q71L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	22420

MSAPAANGEVPTFKLVLVGDGGTGKTTFVKRHLTGEFEKKYIATIGVEVHPLSFYTNFGEIKFDVWDTAGLEKFGGLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDVKERKVKAKTITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLAGNPQLEFVASPALAPPEVQVDEQLMQQYQQEMEQATALPLPDEDDADL

Source Source

Source organism organism	Saccharomyces cerevisiae AWRI796
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	764097
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	Ran-specific GTPase-activating protein 2
Molecular weight formula_weight	26237.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EDDKKEDKFVFGAASKFGTGFGVAKKDTKDGDATTSTESLPASDSKTKKPFAFGSGLSFGSGFNILKNKTENNSESEKKATDVDKDKVHSGSEQLANASEDTKDKPKPLKLQKQEVKSGEESEECIYQVNAKLYQLSNIKEGWKERGVGIIKINKSKDDVEKTRIVMRSRGILKVILNIQLVKGFTVQKGFTGSLQSEKFIRLLAVDDNGDPAQYAIKTGKKETTDELYNIIVKSVPK

Source Source

Source organism organism	Saccharomyces cerevisiae 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	Exportin-1
Molecular weight formula_weight	120398.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREFVKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLLDLTVKKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRTVILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQYKDLVVFKGTLRDFLVQIKEVGGDPTDYLFAEDKENALMEQNRLEREKAAKIGGLLKPSELDD

Source Source

Source organism organism	Saccharomyces cerevisiae 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 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	888

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3wyfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3wyfB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	3wyfC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	3wyfC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	3wyfD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3wyfE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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Unit-cell length a length_a	87.490 Å
Unit-cell length b length_b	155.950 Å
Unit-cell length c length_c	149.820 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.220 Å
Low-resolution limit resolution_low	33.690 Å
R factor r_factor	0.1770
R_work r_work	0.1750
R_free r_free	0.2140

Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex

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

Gsp1p

State in the Current Structure

Other States of the Same Protein in the Database

Ran-specific GTPase-activating protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Exportin-1

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

3wyf__assembly_1__model_1

3wyf__assembly_1__model_1 | I(q)

3wyf__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex

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

Gsp1p

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ran-specific GTPase-activating protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Exportin-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

3wyf__assembly_1__model_1

3wyf__assembly_1__model_1 | I(q)

3wyf__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)