3h90

Structural basis for the autoregulation of the zinc transporter YiiP

Method: X-RAY DIFFRACTION

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

Ferrous-iron efflux pump fieF

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MERCURY (II) ION × 4 ZINC ION × 8 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MERCURY (II) ION × 4 ZINC ION × 8 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FIEF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 8–290 Author chain B； PDBConstruct 1–283； UniProt 8–290 Author chain C； PDBConstruct 1–283； UniProt 8–290 Author chain D； PDBConstruct 1–283； UniProt 8–290

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	3h90
Deposition date deposition_date	2009-04-29
Structure title title	Structural basis for the autoregulation of the zinc transporter YiiP
Keywords keywords	;membrane protein, zinc transporter, Cell inner membrane, Cell membrane, Ion transport, Iron, Iron transport, Membrane, Transmembrane, Transport, TRANSPORT PROTEIN ;; 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.

3h90__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3h90__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3h90__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.72 Å
Rg (electron density)	29.57 Å
Total Rg	30.32 Å
Atom count	4368
Residues	566
Excluded volume	78947 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3h90__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3h90__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Ferrous-iron efflux pump fieF
Molecular weight formula_weight	30973.9 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	9001

LVSRAAIAATAMASLLLLIKIFAWWYTGSVSILAALVDSLVDIGASLTNLLVVRYSLQPADDNHSFGHGKAESLAALAQSMFISGSALFLFLTGIQHLISPTPMTDPGVGVIVTIVALICTIILVSFQRWVVRRTQSQAVRADMLHYQSDVMMNGAILLALGLSWYGWHRADALFALGIGIYILYSALRMGYEAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQIHLEMEDSLPLVQAHMVADQVEQAILRRFPGSDVIIHQDPCSVV

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3h90a1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.59 — Cation efflux protein transmembrane domain-like
Superfamily Superfamily superfamily	f.59.1 — Cation efflux protein transmembrane domain-like
Family Family family	f.59.1.1 — Cation efflux protein transmembrane domain-like

Domain ID domain_id	d3h90a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.9 — Cation efflux protein cytoplasmic domain-like
Family Family family	d.52.9.0 — automated matches

Domain ID domain_id	d3h90b1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.59 — Cation efflux protein transmembrane domain-like
Superfamily Superfamily superfamily	f.59.1 — Cation efflux protein transmembrane domain-like
Family Family family	f.59.1.1 — Cation efflux protein transmembrane domain-like

Domain ID domain_id	d3h90b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.9 — Cation efflux protein cytoplasmic domain-like
Family Family family	d.52.9.0 — automated matches

Domain ID domain_id	d3h90c1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.59 — Cation efflux protein transmembrane domain-like
Superfamily Superfamily superfamily	f.59.1 — Cation efflux protein transmembrane domain-like
Family Family family	f.59.1.1 — Cation efflux protein transmembrane domain-like

Domain ID domain_id	d3h90c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.9 — Cation efflux protein cytoplasmic domain-like
Family Family family	d.52.9.0 — automated matches

Domain ID domain_id	d3h90d1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.59 — Cation efflux protein transmembrane domain-like
Superfamily Superfamily superfamily	f.59.1 — Cation efflux protein transmembrane domain-like
Family Family family	f.59.1.1 — Cation efflux protein transmembrane domain-like

Domain ID domain_id	d3h90d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.9 — Cation efflux protein cytoplasmic domain-like
Family Family family	d.52.9.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3h90A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1510 — Alpha-lytic protease prodomain-like
Homologous superfamily homologous superfamily	10 — Cation efflux protein transmembrane domain

Domain ID domain_id	3h90A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1350 — Cation efflux protein, cytoplasmic domain

Domain ID domain_id	3h90B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1510 — Alpha-lytic protease prodomain-like
Homologous superfamily homologous superfamily	10 — Cation efflux protein transmembrane domain

Domain ID domain_id	3h90B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1350 — Cation efflux protein, cytoplasmic domain

Domain ID domain_id	3h90C01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1510 — Alpha-lytic protease prodomain-like
Homologous superfamily homologous superfamily	10 — Cation efflux protein transmembrane domain

Domain ID domain_id	3h90C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1350 — Cation efflux protein, cytoplasmic domain

Domain ID domain_id	3h90D01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1510 — Alpha-lytic protease prodomain-like
Homologous superfamily homologous superfamily	10 — Cation efflux protein transmembrane domain

Domain ID domain_id	3h90D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1350 — Cation efflux protein, cytoplasmic domain

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Unit-cell length a length_a	105.657 Å
Unit-cell length b length_b	130.704 Å
Unit-cell length c length_c	115.757 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2613
R_free r_free	0.2768

Structural basis for the autoregulation of the zinc transporter YiiP

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

Ferrous-iron efflux pump fieF

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

3h90__assembly_2__model_1

3h90__assembly_2__model_1 | I(q)

3h90__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structural basis for the autoregulation of the zinc transporter YiiP

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

Ferrous-iron efflux pump fieF

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

3h90__assembly_2__model_1

3h90__assembly_2__model_1 | I(q)

3h90__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)