SAXSdb — 3gi9

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

Uncharacterized protein MJ0609

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	7F11 Anti-ApcT Monoclonal Fab Light Chain × 1 7F11 Anti-ApcT Monoclonal Fab Heavy Chain × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y609_METJA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–435； UniProt 1–435

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	3gi9
Deposition date deposition_date	2009-03-05
Structure title title	Crystal Structure of ApcT Transporter Bound to 7F11 Monoclonal Fab Fragment
Keywords keywords	;membrane protein, transporter, antibody, Cell membrane, Membrane, Transmembrane, TRANSPORT PROTEIN, Structural Genomics, PSI-2, Protein Structure Initiative, New York Consortium on Membrane Protein Structure, NYCOMPS ;; 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.

3gi9__assembly_1__model_1

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

Download this curve (.dat)

3gi9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gi9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.68 Å
Rg (electron density)	37.27 Å
Total Rg	37.49 Å
Atom count	6714
Residues	873
Excluded volume	121460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gi9__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 (4)

Entity 1 Entity 1 polymer

Description description	7F11 Anti-ApcT Monoclonal Fab Light Chain
Molecular weight formula_weight	24284.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	6865

DIVMTQSPSSLAMSVGQKVTLSCKSSQSLLNTSNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLSDFFCQQHYSTPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Mus musculus

Entity 2 Entity 2 polymer

Description description	7F11 Anti-ApcT Monoclonal Fab Heavy Chain
Molecular weight formula_weight	23984.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLLQPGAELVKPGASVKLSCKASGYTFTSYWMYWVKQRPGQGLEWIGEIDPSDSYTNYNQNFKGKATLTVDKSSSTAFMQLSSLTSQDSAVYFCARSPHYYGTTYNYPMDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	Uncharacterized protein MJ0609
Molecular weight formula_weight	48330.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MELKNKKLSLWEAVSMAVGVMIGASIFSIFGVGAKIAGRNLPETFILSGIYALLVAYSYTKLGAKIVSNAGPIAFIHKAIGDNIITGALSILLWMSYVISIALFAKGFAGYFLPLINAPINTFNIAITEIGIVAFFTALNFFGSKAVGRAEFFIVLVKLLILGLFIFAGLITIHPSYVIPDLAPSAVSGMIFASAIFFLSYMGFGVITNASEHIENPKKNVPRAIFISILIVMFVYVGVAISAIGNLPIDELIKASENALAVAAKPFLGNLGFLLISIGALFSISSAMNATIYGGANVAYSLAKDGELPEFFERKVWFKSTEGLYITSALGVLFALLFNMEGVASITSAVFMVIYLFVILSHYILIDEVGGRKEIVIFSFIVVLGVFLLLLYYQWITNRFVFYGIIATFIGVLIFEIIYRKVTKRTFSNNMYVKSLESSGLVPR

Source Source

Source organism organism	Methanocaldococcus jannaschii
Common name common_name	Methanococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	151

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3gi9c1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.54 — SNF-like
Superfamily Superfamily superfamily	f.54.1 — SNF-like
Family Family family	f.54.1.2 — Amino acid antiporter-like

Domain ID domain_id	d3gi9c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3gi9h_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3gi9l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d3gi9l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	3gi9C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1740 — Amino acid/polyamine transporter I
Homologous superfamily homologous superfamily	10 — Amino acid/polyamine transporter I

Domain ID domain_id	3gi9H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3gi9H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3gi9L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3gi9L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	148.365 Å
Unit-cell length b length_b	45.900 Å
Unit-cell length c length_c	158.088 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.480 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2503
R_work r_work	0.2479
R_free r_free	0.2957

Crystal Structure of ApcT Transporter Bound to 7F11 Monoclonal Fab Fragment

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

Uncharacterized protein MJ0609

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

3gi9__assembly_1__model_1

3gi9__assembly_1__model_1 | I(q)

3gi9__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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal Structure of ApcT Transporter Bound to 7F11 Monoclonal Fab Fragment

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

Uncharacterized protein MJ0609

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

3gi9__assembly_1__model_1

3gi9__assembly_1__model_1 | I(q)

3gi9__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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)