SAXSdb — 6tyl

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

Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Nanobody A × 1 Nanobody B × 1 Nanobody C × 1 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 （P10824）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Nanobody A × 1 Nanobody B × 1 Nanobody C × 1 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 （P10824）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1H241_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–492； UniProt 1–491 Author chain F； PDBConstruct 2–492； UniProt 1–491

Guanine nucleotide-binding protein G(i) subunit alpha-1

Rattus norvegicus

UniProt P10824

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans) × 1 （B1H241） Nanobody A × 1 Nanobody B × 1 Nanobody C × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans) × 1 （B1H241） Nanobody A × 1 Nanobody B × 1 Nanobody C × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GNAI1_RAT
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–354； UniProt 1–354 Author chain G； PDBConstruct 1–354； UniProt 1–354

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	6tyl
Deposition date deposition_date	2019-08-09
Structure title title	Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex
Keywords keywords	Ric-8A, G protein, GEF, SIGNALING PROTEIN; SIGNALING 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.

6tyl__assembly_1__model_1

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

Download this curve (.dat)

6tyl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6tyl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.94 Å
Rg (electron density)	36.05 Å
Total Rg	36.50 Å
Atom count	7993
Residues	1011
Excluded volume	141800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6tyl__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6tyl__assembly_2__model_1`	pentameric （5）	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	Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
Molecular weight formula_weight	55836.9 kDa
Mutation mutation	Y232F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	15938

GMEPRAVADALETGEEDAVTEALRSFNREHSQSFTFDDAQQEDRKRLAKLLVSVLEQGLSPKHRVTWLQTIRILSRDRSCLDSFASRQSLHALACYADIAISEEPIPQPPDMDVLLESLKCLCNLVLSSPTAQMLAAEARLVVRLAERVGLYRKRSYPHEVQFFDLRLLFLLTALRTDVRQQLFQELHGVRLLTDALELTLGVAPKENPLVILPAQETERAMEILKVLFNITFDSVKREVDEEDAALYRYLGTLLRHCVMADAAGDRTEEFHGHTVNLLGNLPLKCLDVLLALELHEGSLEFMGVNMDVINALLAFLEKRLHQTHRLKECVAPVLSVLTECARMHRPARKFLKAQVLPPLRDVRTRPEVGDLLRNKLVRLMTHLDTDVKRVAAEFLFVLCSESVPRFIKYTGYGNAAGLLAARGLMAGGRPEGQYSEDEDTDTEEYREAKASINPVTGRVEEKPPNPMEGMTEEQKEHEAMKLVNMFDKLSR

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nanobody A
Molecular weight formula_weight	13609.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVQLQESGGGLVQPGGSLRLSCAASGIIFRSNGMAWYRQAPGKEREWVASITSFGDAIYRDSVKGRFTISRDNARNAVSLQTNSLKTEDTAVYYCNTYPVNSAWGQGTQVTVSSHHHHHHEPEA

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nanobody B
Molecular weight formula_weight	14247.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVQLQESGGGLVQAGGSLRLSCAASGGIVHISSMGWFRQAPGKQRELVATSPSNGDIRYADSVKGRFTLSRDNAKNTVSLQMNSLEPEDTAVYYCHSFLRHTASASYNNYYGQGTQVTVSSHHHHHHEPEA

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Nanobody C
Molecular weight formula_weight	14894.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I

QVQLQESGGGLEQAGDSLRLSCAASGLIVSNYAMGWFRQAPGKEREFVAYINWNGGVTYYTNSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCARTSRASVTTRVADFGYWGQGTQVTVSSHHHHHHEPEA

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Guanine nucleotide-binding protein G(i) subunit alpha-1
Molecular weight formula_weight	40399.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6tylA01
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	6tylF01
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

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Unit-cell length a length_a	93.048 Å
Unit-cell length b length_b	144.726 Å
Unit-cell length c length_c	114.420 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.66 °
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	monoclinic

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	39.530 Å
R factor r_factor	—
R_work r_work	0.2480
R_free r_free	0.2870

Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex

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

Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)

State in the Current Structure

Other States of the Same Protein in the Database

Guanine nucleotide-binding protein G(i) subunit alpha-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

6tyl__assembly_1__model_1

6tyl__assembly_1__model_1 | I(q)

6tyl__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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of mammalian Ric-8A:Galpha(i):nanobody complex

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

Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Guanine nucleotide-binding protein G(i) subunit alpha-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

6tyl__assembly_1__model_1

6tyl__assembly_1__model_1 | I(q)

6tyl__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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)