3gd3

Crystal structure of a naturally folded murine apoptosis inducing factor

Method: X-RAY DIFFRACTION

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

Apoptosis-inducing factor 1, mitochondrial

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AIFM1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–535； UniProt 78–612 Author chain B； PDBConstruct 1–535； UniProt 78–612 Author chain C； PDBConstruct 1–535； UniProt 78–612 Author chain D； PDBConstruct 1–535； UniProt 78–612

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	3gd3
Deposition date deposition_date	2009-02-23
Structure title title	Crystal structure of a naturally folded murine apoptosis inducing factor
Keywords keywords	;alpha and beta protein, Acetylation, Apoptosis, DNA-binding, FAD, Flavoprotein, Mitochondrion, Nucleus, Oxidoreductase, Phosphoprotein, Transit peptide ;; OXIDOREDUCTASE
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.

3gd3__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gd3__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gd3__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	23.92 Å
Rg (electron density)	22.80 Å
Total Rg	23.78 Å
Atom count	3632
Residues	465
Excluded volume	64492 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gd3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gd3__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gd3__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3gd3__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3gd3__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3gd3__assembly_6__model_1`	monomeric （1）	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	Apoptosis-inducing factor 1, mitochondrial
Molecular weight formula_weight	58328.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14717

GAGAYAYKTIKEDQKRYNERVMGLGLSPEEKQRRAIASATEGGSVPQIRAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLQFRQWNGKERSIYFQPPSFYVSAQDLPNIENGGVAVLTGKKVVHLDVRGNMVKLNDGSQITFEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRALEKISREVKSITVIGGGFLGSELACALGRKSQASGIEVIQLFPEKGNMGKILPQYLSNWTMEKVKREGVKVMPNAIVQSVGVSGGRLLIKLKDGRKVETDHIVTAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSESETESEASEITIPPSAPAVPQVPVEGEDYGKGVIFYLRDKVVVGIVLWNVFNRMPIARKIIKDGEQHEDLNEVAKLFNIHED

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Apoptosis-inducing factor 1, mitochondrial
Molecular weight formula_weight	784.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

XXXXXXXXX

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3gd3A01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3A02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	3gd3B01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3B02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	3gd3C01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3C02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3C03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	3gd3D01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3D02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gd3D03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

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Unit-cell length a length_a	75.050 Å
Unit-cell length b length_b	80.290 Å
Unit-cell length c length_c	419.640 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	46.640 Å
R factor r_factor	0.2510
R_work r_work	0.2486
R_free r_free	0.2997

Crystal structure of a naturally folded murine apoptosis inducing factor

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

Apoptosis-inducing factor 1, mitochondrial

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

3gd3__assembly_4__model_1

3gd3__assembly_4__model_1 | I(q)

3gd3__assembly_4__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of a naturally folded murine apoptosis inducing factor

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

Apoptosis-inducing factor 1, mitochondrial

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

3gd3__assembly_4__model_1

3gd3__assembly_4__model_1 | I(q)

3gd3__assembly_4__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)