5vpn

E. coli Quinol fumarate reductase FrdA E245Q mutation

Method: X-RAY DIFFRACTION

▼

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

Fumarate reductase flavoprotein subunit

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase iron-sulfur subunit × 1 （A0A076YHN1） Fumarate reductase subunit C × 1 （P0A8Q0） Fumarate reductase subunit D × 1 （P0A8Q3） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase iron-sulfur subunit × 1 （A0A076YHN1） Fumarate reductase subunit C × 1 （P0A8Q0） Fumarate reductase subunit D × 1 （P0A8Q3） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FRDA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–585； UniProt 1–585 Author chain E； PDBConstruct 1–585； UniProt 1–585

Succinate dehydrogenase iron-sulfur subunit

Escherichia coli

UniProt A0A076YHN1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （P00363） Fumarate reductase subunit C × 1 （P0A8Q0） Fumarate reductase subunit D × 1 （P0A8Q3） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （P00363） Fumarate reductase subunit C × 1 （P0A8Q0） Fumarate reductase subunit D × 1 （P0A8Q3） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A076YHN1_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–243； UniProt 17–259 Author chain F； PDBConstruct 1–243； UniProt 17–259

Fumarate reductase subunit C

Escherichia coli (strain K12)

UniProt P0A8Q0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （P00363） Succinate dehydrogenase iron-sulfur subunit × 1 （A0A076YHN1） Fumarate reductase subunit D × 1 （P0A8Q3） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （P00363） Succinate dehydrogenase iron-sulfur subunit × 1 （A0A076YHN1） Fumarate reductase subunit D × 1 （P0A8Q3） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FRDC_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–130； UniProt 2–131 Author chain G； PDBConstruct 1–130； UniProt 2–131

Fumarate reductase subunit D

Escherichia coli (strain K12)

UniProt P0A8Q3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （P00363） Succinate dehydrogenase iron-sulfur subunit × 1 （A0A076YHN1） Fumarate reductase subunit C × 1 （P0A8Q0） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （P00363） Succinate dehydrogenase iron-sulfur subunit × 1 （A0A076YHN1） Fumarate reductase subunit C × 1 （P0A8Q0） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FRDD_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–119； UniProt 1–119 Author chain H； PDBConstruct 1–119； UniProt 1–119

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5vpn
Deposition date deposition_date	2017-05-05
Structure title title	E. coli Quinol fumarate reductase FrdA E245Q mutation
Keywords keywords	quinol fumarate reductase, fumarate reduction, membrane protein, Complex II Superfamily, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5vpn__assembly_2__model_1

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

Download this curve (.dat)

5vpn__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vpn__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	32.64 Å
Rg (electron density)	33.38 Å
Total Rg	33.45 Å
Atom count	8453
Residues	1077
Excluded volume	150900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vpn__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vpn__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Fumarate reductase flavoprotein subunit
Molecular weight formula_weight	64339.7 kDa
EC 编号 ec_number	1.3.5.4
Mutation mutation	E245Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	16845

MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDHDSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGMKIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGTLVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGSGILMTQGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWRKGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMGGIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGNGNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKLAELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGCTERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEA

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Succinate dehydrogenase iron-sulfur subunit
Molecular weight formula_weight	27021.9 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AEMKNLKIEVVRYNPEVDTAPHSAFYEVPYDATTSLLDALGYIKDNLAPDLSYRWSCRMAICGSCGMMVNNVPKLACKTFLRDYTDGMKVEALANFPIERDLVVDMTHFIESLEAIKPYIIGNSRTADQGTNIQTPAQMAKYHQFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHVDPAAAIQQGKVESSKDFLIATLKPR

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	Fumarate reductase subunit C
Molecular weight formula_weight	14898.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TTKRKPYVRPMTSTWWKKLPFYRFYMLREGTAVPAVWFSIELIFGLFALKNGPEAWAGFVDFLQNPVIVIINLITLAAALLHTKTWFELAPKAANIIVKDEKMGPEPIIKSLWAVTVVATIVILFVALYW

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Fumarate reductase subunit D
Molecular weight formula_weight	13118.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MINPNPKRSDEPVFWGLFGAGGMWSAIIAPVMILLVGILLPLGLFPGDALSYERVLAFAQSFIGRVFLFLMIVLPLWCGLHRMHHAMHDLKIHVPAGKWVFYGLAAILTVVTLIGVVTI

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

▶

Unit-cell length a length_a	133.565 Å
Unit-cell length b length_b	138.134 Å
Unit-cell length c length_c	220.079 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	8

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

Resolution resolution	4.223 Å
Low-resolution limit resolution_low	22.962 Å
R factor r_factor	0.2176
R_work r_work	0.2148
R_free r_free	0.2704

E. coli Quinol fumarate reductase FrdA E245Q mutation

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

Fumarate reductase flavoprotein subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Succinate dehydrogenase iron-sulfur subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fumarate reductase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fumarate reductase subunit D

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

5vpn__assembly_2__model_1

5vpn__assembly_2__model_1 | I(q)

5vpn__assembly_2__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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)