SAXSdb — 6q84

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

Importin beta-like protein KAP122

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 3	GTP-binding nuclear protein Ran × 1 （P62826） Eukaryotic translation initiation factor 5A-1 × 1 （P23301） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	GTP-binding nuclear protein Ran × 1 （P62826） Eukaryotic translation initiation factor 5A-1 × 1 （P23301） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KA122_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1080； UniProt 2–1081 Author chain D； PDBConstruct 1–1080； UniProt 2–1081

GTP-binding nuclear protein Ran

Homo sapiens

UniProt P62826

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Importin beta-like protein KAP122 × 1 （P32767） Eukaryotic translation initiation factor 5A-1 × 1 （P23301） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Importin beta-like protein KAP122 × 1 （P32767） Eukaryotic translation initiation factor 5A-1 × 1 （P23301） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–176； UniProt 5–180 Author chain E； PDBConstruct 1–176； UniProt 5–180

Eukaryotic translation initiation factor 5A-1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P23301

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Importin beta-like protein KAP122 × 1 （P32767） GTP-binding nuclear protein Ran × 1 （P62826） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Importin beta-like protein KAP122 × 1 （P32767） GTP-binding nuclear protein Ran × 1 （P62826） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF5A1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–142； UniProt 16–157 Author chain F； PDBConstruct 1–142； UniProt 16–157

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	6q84
Deposition date deposition_date	2018-12-14
Structure title title	Crystal structure of RanGTP-Pdr6-eIF5A export complex
Keywords keywords	Importin-Beta family, biportin, nuclear export, translation factor, 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.

6q84__assembly_1__model_1

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

Download this curve (.dat)

6q84__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6q84__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.93 Å
Rg (electron density)	35.04 Å
Total Rg	35.65 Å
Atom count	10644
Residues	1327
Excluded volume	191330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6q84__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6q84__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 (5)

Entity 1 Entity 1 polymer

Description description	Importin beta-like protein KAP122
Molecular weight formula_weight	123492.6 kDa
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	21207

SSIHEVVALIEELYSPHPKHDVNQIQQSLQSIQKSEQGFHLANELLSDDKYSANVKYFGALTLTVQLNTRGENDYETLWNVFRSNLLYLTKFSTLYVSNPNMYGQSLIIIKKLMSNLSLIFTKINDPQLNNAGNENMIKQWNNPINTFIQLMSVQNQNINADQLLLDSINCSLTYEQLSQFVSLSQKHNELALTFTEVIVEDLTKFQTKRHSMSQIHEVVHEHLYISTMALINLNLTAQAVFNPTVFDCITAWINYISLTRSVSSSGRMDLSEIFQNLIDLMYQSTEGSDGYENAEKILTIFGNVFANDPLLMSYDLRQQIECIFLGVVRPDSGITDISNKNSWMLQYMNYLVTNDFFSELKELAICIVDFLQINTLSVCNKLFTNIQAADNGQVQDEYIQEYIKVLLQMTNFPLTPVLQEFFSVRMVDFWLDLSDAYTNLASETLRPNSIELSTQIFQQLINIYLPKISLSVKQRIIEEEGESTSVNEFEDFRNAVSDLAQSLWSILGNDNLTNVLIDGMGQMPAASDETLIIKDTDVLFRIETMCFVLNTILVDMTLSESPWIKNIVDANKFFNQNVISVFQTGFQTSASTKVSQILKLDFVRTSTTLIGTLAGYFKQEPFQLNPYVEALFQGLHTCTNFTSKNEQEKISNDKLEVMVIKTVSTLCETCREELTPYLMHFISFLNTVIMPDSNVSHFTRTKLVRSIGYVVQCQVSNGPEEQAKYILQLTNLLSGSIEHCLASSVQLQEQQDYINCLLYCISELATSLIQPTEIIENDALLQRLSEFQSFWSSDPLQIRSKIMCTIDKVLDNSIYCKNSAFVEIGCLIVGKGLNLPDGEPYFLKYNMSEVMNFVLRHVPNCELATCLPYFVYLLEKLISEFRKELTPQEFDFMFEKILLVYYDAYIINDPDLLQMTIGFVNNVLDVKPGLAIGSKHWTSFILPQFLKLIPSREKFTIVAVAKFWTKLINNKKYNQEELTTVRQQVSSIGGDLVYQIMYGLFHTQRSDLNSYTDLLRALVAKFPIEAREWLVAVLPQICNNPAGHEKFINKLLITRGSRAAGNVILQWWLDCTTLPNYQG

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	GTP-binding nuclear protein Ran
Molecular weight formula_weight	20192.5 kDa
Mutation mutation	Q69L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP

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 3 Entity 3 polymer

Description description	Eukaryotic translation initiation factor 5A-1
Molecular weight formula_weight	15526.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHLVAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDIDDGFLSLMNMDGDTKDDVKAPEGELGDSLQTAFDEGKDLMVTIISAMGEEAAISFKEAARTD

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 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

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6q84B00
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	6q84C01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6q84C02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	6q84E00
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	6q84F01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6q84F02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	139.540 Å
Unit-cell length b length_b	139.540 Å
Unit-cell length c length_c	346.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.700 Å
Low-resolution limit resolution_low	49.173 Å
R factor r_factor	0.2273
R_work r_work	0.2065
R_free r_free	0.2471

Crystal structure of RanGTP-Pdr6-eIF5A export complex

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

Importin beta-like protein KAP122

State in the Current Structure

Other States of the Same Protein in the Database

GTP-binding nuclear protein Ran

State in the Current Structure

Other States of the Same Protein in the Database

Eukaryotic translation initiation factor 5A-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

6q84__assembly_1__model_1

6q84__assembly_1__model_1 | I(q)

6q84__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 (5)

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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of RanGTP-Pdr6-eIF5A export complex

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

Importin beta-like protein KAP122

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

Eukaryotic translation initiation factor 5A-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

6q84__assembly_1__model_1

6q84__assembly_1__model_1 | I(q)

6q84__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 (5)

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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)