4f1e

The Crystal Structure of a Human MitoNEET mutant with Asp 67 replaced by a Gly

Method: X-RAY DIFFRACTION

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

CDGSH iron-sulfur domain-containing protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 1	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	FE2/S2 (INORGANIC) CLUSTER × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CISD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 33–108 Author chain B； PDBConstruct 1–76； UniProt 33–108 Author chain C； PDBConstruct 1–76； UniProt 33–108 Author chain D； PDBConstruct 1–76； UniProt 33–108 Author chain E； PDBConstruct 1–76； UniProt 33–108 Author chain F； PDBConstruct 1–76； UniProt 33–108 Author chain G； PDBConstruct 1–76； UniProt 33–108 Author chain H； PDBConstruct 1–76； UniProt 33–108 Author chain I； PDBConstruct 1–76； UniProt 33–108 Author chain J； PDBConstruct 1–76； UniProt 33–108 Author chain K； PDBConstruct 1–76； UniProt 33–108 Author chain L； PDBConstruct 1–76； UniProt 33–108 Author chain M； PDBConstruct 1–76； UniProt 33–108 Author chain N； PDBConstruct 1–76； UniProt 33–108 Author chain O； PDBConstruct 1–76； UniProt 33–108 Author chain P； PDBConstruct 1–76； UniProt 33–108 Author chain Q； PDBConstruct 1–76； UniProt 33–108 Author chain R； PDBConstruct 1–76； UniProt 33–108

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	4f1e
Deposition date deposition_date	2012-05-06
Structure title title	The Crystal Structure of a Human MitoNEET mutant with Asp 67 replaced by a Gly
Keywords keywords	ZINC Finger CDGSH-Type domain 1, mitochondrial outer membrane, METAL BINDING PROTEIN; METAL BINDING 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.

4f1e__assembly_4__model_1

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

Download this curve (.dat)

4f1e__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4f1e__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	15.04 Å
Rg (electron density)	14.03 Å
Total Rg	15.02 Å
Atom count	1029
Residues	132
Excluded volume	18345 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4f1e__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4f1e__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4f1e__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4f1e__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4f1e__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4f1e__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4f1e__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`4f1e__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`4f1e__assembly_9__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	CDGSH iron-sulfur domain-containing protein 1
Molecular weight formula_weight	8890.3 kDa
Mutation mutation	D67G
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Atom count atom_count	9244

RFYVKDHRNKAMINLHIQKDNPKIVHAFDMEDLGGKAVYCRCWRSKKFPFCDGAHTKHNEETGDNVGPLIIKKKET

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 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d4f1ea_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1eb_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ec_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ed_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ee_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ef_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1eg_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1eh_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ei_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ej_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ek_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1el_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1em_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1en_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1eo_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1ep_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1eq_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

Domain ID domain_id	d4f1er_
Class class	g — Small proteins
Fold Fold fold	g.97 — Iron-sulfur cluster-binding zinc finger CDGSH type
Superfamily Superfamily superfamily	g.97.1 — Iron-sulfur cluster-binding zinc finger CDGSH type
Family Family family	g.97.1.1 — Outer mitochondrial membrane protein mitoNEET-like

CATH v4.4 (18 domains)

Domain ID domain_id	4f1eA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eN01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eO01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eP01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eQ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

Domain ID domain_id	4f1eR01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	90 — CDGSH iron-sulfur domain, mitoNEET-type

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Unit-cell length a length_a	56.396 Å
Unit-cell length b length_b	110.855 Å
Unit-cell length c length_c	207.294 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	72

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	49.540 Å
R factor r_factor	0.1950
R_work r_work	0.1933
R_free r_free	0.2272

The Crystal Structure of a Human MitoNEET mutant with Asp 67 replaced by a Gly

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

CDGSH iron-sulfur domain-containing protein 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

4f1e__assembly_4__model_1

4f1e__assembly_4__model_1 | I(q)

4f1e__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

CATH v4.4 (18 domains)

7. Citations (1)

The Crystal Structure of a Human MitoNEET mutant with Asp 67 replaced by a Gly

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

CDGSH iron-sulfur domain-containing 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4f1e__assembly_4__model_1

4f1e__assembly_4__model_1 | I(q)

4f1e__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

CATH v4.4 (18 domains)

7. Citations (1)