5ytb

RanY197A in complex with RanBP1-CRM1

Method: X-RAY DIFFRACTION

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

GTP-binding nuclear protein Ran

Homo sapiens

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 1 × 1 （P41920） Exportin-1,Exportin-1 × 1 （P30822） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 1 CHLORIDE ION × 7 GLYCEROL × 3 ACETATE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 1–216

Ran-specific GTPase-activating protein 1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P41920

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	GTP-binding nuclear protein Ran × 1 （P62826） Exportin-1,Exportin-1 × 1 （P30822） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 1 CHLORIDE ION × 7 GLYCEROL × 3 ACETATE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YRB1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–139； UniProt 62–200

Exportin-1,Exportin-1

Saccharomyces cerevisiae

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	GTP-binding nuclear protein Ran × 1 （P62826） Ran-specific GTPase-activating protein 1 × 1 （P41920） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 1 CHLORIDE ION × 7 GLYCEROL × 3 ACETATE ION × 2 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 3–378； UniProt 1–376 Author chain C； PDBConstruct 379–1017； UniProt 414–1052

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	5ytb
Deposition date deposition_date	2017-11-17
Structure title title	RanY197A in complex with RanBP1-CRM1
Keywords keywords	Active Ran, Complex, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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.

5ytb__assembly_1__model_1

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

Download this curve (.dat)

5ytb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ytb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.05 Å
Rg (electron density)	35.24 Å
Total Rg	35.83 Å
Atom count	10933
Residues	1347
Excluded volume	196420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ytb__assembly_1__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 (10)

Entity 1 Entity 1 polymer

Description description	GTP-binding nuclear protein Ran
Molecular weight formula_weight	24364.0 kDa
Mutation mutation	Y197A
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	11162

MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQAEHDLEVAQTTALPDEDDDL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ran-specific GTPase-activating protein 1
Molecular weight formula_weight	16249.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIHFEPVVHLEKVDVKTMEEDEEVLYKVRAKLFRFDADAKEWKERGTGDCKFLKNKKTNKVRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSKENADKFKEEFEKAQEINKK

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	Exportin-1,Exportin-1
Molecular weight formula_weight	116682.1 kDa
Mutation mutation	D537G, T539C, V540E, K541Q, Y1022C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREFVKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLLGLCEQKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRTVILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFA

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 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	1

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	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	229

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ytba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d5ytbb_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5ytbA00
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	5ytbB00
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	105.285 Å
Unit-cell length b length_b	105.285 Å
Unit-cell length c length_c	305.726 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1906
R_work r_work	0.1886
R_free r_free	0.2291

RanY197A in complex with RanBP1-CRM1

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

GTP-binding nuclear protein Ran

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 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

Exportin-1,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

5ytb__assembly_1__model_1

5ytb__assembly_1__model_1 | I(q)

5ytb__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 (10)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)