2qi9

ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF

Method: X-RAY DIFFRACTION

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

Vitamin B12 import system permease protein btuC

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Vitamin B12 import ATP-binding protein btuD × 2 （P06611） Vitamin B12-binding protein btuF × 1 （P37028） PHOSPHATE ION × 2 SULFATE ION × 6 PENTAETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BTUC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 1–326 Author chain B； PDBConstruct 1–326； UniProt 1–326

Vitamin B12 import ATP-binding protein btuD

Escherichia coli

UniProt P06611

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Vitamin B12 import system permease protein btuC × 2 （P06609） Vitamin B12-binding protein btuF × 1 （P37028） PHOSPHATE ION × 2 SULFATE ION × 6 PENTAETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BTUD_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain D； PDBConstruct 1–249； UniProt 1–249

Vitamin B12-binding protein btuF

Escherichia coli

UniProt P37028

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Vitamin B12 import system permease protein btuC × 2 （P06609） Vitamin B12 import ATP-binding protein btuD × 2 （P06611） PHOSPHATE ION × 2 SULFATE ION × 6 PENTAETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BTUF_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–245； UniProt 22–266

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	2qi9
Deposition date deposition_date	2007-07-03
Structure title title	ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF
Keywords keywords	Inner membrane, Membrane, Transmembrane, Transport, ATP-binding, Hydrolase, Nucleotide-binding, Periplasm, MEMBRANE PROTEIN; MEMBRANE 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.

2qi9__assembly_1__model_1

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

Download this curve (.dat)

2qi9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qi9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.28 Å
Rg (electron density)	37.63 Å
Total Rg	37.89 Å
Atom count	10676
Residues	1349
Excluded volume	193400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qi9__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	Vitamin B12 import system permease protein btuC
Molecular weight formula_weight	35375.5 kDa
Mutation mutation	C18S, C32S, C120S, C156S, C205S, C206S, C267S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10692

MLTLARQQQRQNIRWLLSLSVLMLLALLLSLSAGEQWISPGDWFTPRGELFVWQIRLPRTLAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQGQLPNWALGLSAIAGALIITLILLRFARRHLSTSRLLLAGVALGIISSALMTWAIYFSTSVDLRQLMYWMMGGFGGVDWRQSWLMLALIPVLLWISSQSRPMNMLALGEISARQLGLPLWFWRNVLVAATGWMVGVSVALAGAIGFIGLVIPHILRLSGLTDHRVLLPGCALAGASALLLADIVARLALAAAELPIGVVTATLGAPVFIWLLLKAGR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Vitamin B12 import ATP-binding protein btuD
Molecular weight formula_weight	27520.2 kDa
EC 编号 ec_number	3.6.3.33
Mutation mutation	C180S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSIVMQLQDVAESTRLGPLSGEVRAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAGQPLEAWSATKLALHRAYLSQQQTPPFATPVWHYLTLHQHDKTRTELLNDVAGALALDDKLGRSTNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDEPMNSLDVAQQSALDKILSALSQQGLAIVMSSHDLNHTLRHAHRAWLLKGGKMLASGRREEVLTPPNLAQAYGMNFRRLDIEGHRMLISTI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Vitamin B12-binding protein btuF
Molecular weight formula_weight	27140.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

AAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2qi9a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.22 — ABC transporter involved in vitamin B12 uptake, BtuC
Superfamily Superfamily superfamily	f.22.1 — ABC transporter involved in vitamin B12 uptake, BtuC
Family Family family	f.22.1.1 — ABC transporter involved in vitamin B12 uptake, BtuC

Domain ID domain_id	d2qi9b_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.22 — ABC transporter involved in vitamin B12 uptake, BtuC
Superfamily Superfamily superfamily	f.22.1 — ABC transporter involved in vitamin B12 uptake, BtuC
Family Family family	f.22.1.1 — ABC transporter involved in vitamin B12 uptake, BtuC

Domain ID domain_id	d2qi9c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.12 — ABC transporter ATPase domain-like

Domain ID domain_id	d2qi9d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.12 — ABC transporter ATPase domain-like

Domain ID domain_id	d2qi9f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.2 — TroA-like

CATH v4.4 (6 domains)

Domain ID domain_id	2qi9A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3470 — ABC transporter involved in vitamin B12 uptake, BtuC
Homologous superfamily homologous superfamily	10 — ABC transporter involved in vitamin B12 uptake, BtuC

Domain ID domain_id	2qi9B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3470 — ABC transporter involved in vitamin B12 uptake, BtuC
Homologous superfamily homologous superfamily	10 — ABC transporter involved in vitamin B12 uptake, BtuC

Domain ID domain_id	2qi9C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2qi9D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2qi9F01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2qi9F02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

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Unit-cell length a length_a	213.582 Å
Unit-cell length b length_b	127.396 Å
Unit-cell length c length_c	97.547 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.814 Å
R factor r_factor	—
R_work r_work	0.2620
R_free r_free	0.2800

ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF

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

Vitamin B12 import system permease protein btuC

State in the Current Structure

Other States of the Same Protein in the Database

Vitamin B12 import ATP-binding protein btuD

State in the Current Structure

Other States of the Same Protein in the Database

Vitamin B12-binding protein btuF

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

2qi9__assembly_1__model_1

2qi9__assembly_1__model_1 | I(q)

2qi9__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

7. Citations (1)

ABC-transporter BtuCD in complex with its periplasmic binding protein BtuF

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

Vitamin B12 import system permease protein btuC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vitamin B12 import ATP-binding protein btuD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vitamin B12-binding protein btuF

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

2qi9__assembly_1__model_1

2qi9__assembly_1__model_1 | I(q)

2qi9__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

7. Citations (1)