SAXSdb — 4fi3

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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 × 1 （P37028） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 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 24–349； UniProt 1–326 Author chain B； PDBConstruct 24–349； 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 × 1 （P37028） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 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

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） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 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 2–246； 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	4fi3
Deposition date deposition_date	2012-06-07
Structure title title	Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state
Keywords keywords	ABC transporter, Vitamin B12 transport, ATP binding, Membrane, 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.

4fi3__assembly_1__model_1

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

Download this curve (.dat)

4fi3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4fi3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.09 Å
Rg (electron density)	37.48 Å
Total Rg	37.81 Å
Atom count	10635
Residues	1389
Excluded volume	191990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4fi3__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 (5)

Entity 1 Entity 1 polymer

Description description	Vitamin B12 import system permease protein BtuC
Molecular weight formula_weight	37650.6 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	10635

MGHHHHHHHHHHSSGENLYFQGHMLTLARQQQRQNIRWLLSLSVLMLLALLLSLSAGEQWISPGDWFTPRGELFVWQIRLPRTLAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQGQLPNWALGLSAIAGALIITLILLRFARRHLSTSRLLLAGVALGIISSALMTWAIYFSTSVDLRQLMYWMMGGFGGVDWRQSWLMLALIPVLLWISSQSRPMNMLALGEISARQLGLPLWFWRNVLVAATGWMVGVSVALAGAIGFIGLVIPHILRLSGLTDHRVLLPGCALAGASALLLADIVARLALAAAELPIGVVTATLGAPVFIWLLLKAGR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Vitamin B12 import ATP-binding protein BtuD
Molecular weight formula_weight	27086.2 kDa
EC 编号 ec_number	3.6.3.33
Mutation mutation	C180S, E159Q, N162C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSIVMQLQDVAESTRLGPLSGEVRAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAGQPLEAWSATKLALHRAYLSQQQTPPFATPVWHYLTLHQHDKTRTELLNDVAGALALDDKLGRSTNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDQPMCSLDVAQQSALDKILSALSQQGLAIVMSSHDLNHTLRHAHRAWLLKGGKMLASGRREEVLTPPNLAQAYGMNFRRLDIEGHRMLISTI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Vitamin B12-binding protein
Molecular weight formula_weight	28238.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MAAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTWQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGGPDQIPKIKQYWGEQLKIPVIPLTSDWFERASPRIILAAQQLCNALSQVDSGSHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4fi3A00
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	4fi3B00
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	4fi3C00
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	4fi3D00
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	4fi3F01
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	4fi3F02
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	127.730 Å
Unit-cell length b length_b	211.990 Å
Unit-cell length c length_c	179.100 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.466 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2323
R_work r_work	0.2293
R_free r_free	0.2738

Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state

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

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

4fi3__assembly_1__model_1

4fi3__assembly_1__model_1 | I(q)

4fi3__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 (5)

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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state

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

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

4fi3__assembly_1__model_1

4fi3__assembly_1__model_1 | I(q)

4fi3__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 (5)

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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)