9wxb

Cryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH

Method: ELECTRON MICROSCOPY

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

Formate dehydrogenase delta subunit

Rhodobacter aestuarii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Formate dehydrogenase gamma subunit × 2 （A0A1N7KDI2） Formate dehydrogenase alpha subunit × 2 （A0A1N7KDD5） Formate dehydrogenase beta subunit × 2 （A0A1N7KDE1） FE2/S2 (INORGANIC) CLUSTER × 4 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 4 MOLYBDENUM(VI) ION × 2 IRON/SULFUR CLUSTER × 10 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1N7KD80_9RHOB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 1–70； UniProt 1–70 Author chain H； PDBConstruct 1–70； UniProt 1–70

Formate dehydrogenase gamma subunit

Rhodobacter aestuarii

UniProt A0A1N7KDI2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Formate dehydrogenase delta subunit × 2 （A0A1N7KD80） Formate dehydrogenase alpha subunit × 2 （A0A1N7KDD5） Formate dehydrogenase beta subunit × 2 （A0A1N7KDE1） FE2/S2 (INORGANIC) CLUSTER × 4 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 4 MOLYBDENUM(VI) ION × 2 IRON/SULFUR CLUSTER × 10 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1N7KDI2_9RHOB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 30–179； UniProt 1–150 Author chain F； PDBConstruct 30–179； UniProt 1–150

Formate dehydrogenase alpha subunit

Rhodobacter aestuarii

UniProt A0A1N7KDD5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Formate dehydrogenase delta subunit × 2 （A0A1N7KD80） Formate dehydrogenase gamma subunit × 2 （A0A1N7KDI2） Formate dehydrogenase beta subunit × 2 （A0A1N7KDE1） FE2/S2 (INORGANIC) CLUSTER × 4 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 4 MOLYBDENUM(VI) ION × 2 IRON/SULFUR CLUSTER × 10 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1N7KDD5_9RHOB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–957； UniProt 1–957 Author chain B； PDBConstruct 1–957； UniProt 1–957

Formate dehydrogenase beta subunit

Rhodobacter aestuarii

UniProt A0A1N7KDE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Formate dehydrogenase delta subunit × 2 （A0A1N7KD80） Formate dehydrogenase gamma subunit × 2 （A0A1N7KDI2） Formate dehydrogenase alpha subunit × 2 （A0A1N7KDD5） FE2/S2 (INORGANIC) CLUSTER × 4 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE × 4 MOLYBDENUM(VI) ION × 2 IRON/SULFUR CLUSTER × 10 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1N7KDE1_9RHOB
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–501； UniProt 1–501 Author chain D； PDBConstruct 1–501； UniProt 1–501

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	9wxb
Deposition date deposition_date	2025-09-25
Structure title title	Cryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH
Keywords keywords	formate dehydrogenase, formate oxidation, carbon dioxide redcution, FMN, NAD, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

9wxb__assembly_1__model_1

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

Download this curve (.dat)

9wxb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9wxb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.90 Å
Rg (electron density)	50.09 Å
Total Rg	49.67 Å
Atom count	25368
Residues	3324
Excluded volume	448090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9wxb__assembly_1__model_1`	octameric （8）	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 (10)

Entity 1 Entity 1 polymer

Description description	Formate dehydrogenase delta subunit
Molecular weight formula_weight	7180.2 kDa
EC 编号 ec_number	1.17.1.9
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H
Atom count atom_count	25368

MSDEKLIRMANQIAAFFAVQPADRAEGVAAHISDNWAAPMRAALLAHIAAGGAGLDALVVDAAPHIRPAG

Source Source

Source organism organism	Rhodobacter aestuarii
NCBI taxonomy ID ncbi_taxonomy_id	453582
Host organism host_organism	Escherichia coli MC1061

Entity 2 Entity 2 polymer

Description description	Formate dehydrogenase gamma subunit
Molecular weight formula_weight	19331.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SRAWRHPQGGSHHHHHHGMRDLYDDDDKHMTDLARLRAILTAHEGREGALLPILHDVQADYGHIPDAALEPIAKALRLSRAEVAGVVGFYHDFRRSPAGKHVIKLCRAEACQAMGGDGVQARLEAALGLKLGETKHDITLEAAYCLGLCACAPAAMVNDALVGRLDDAAVDTIAAEVRA

Source Source

Source organism organism	Rhodobacter aestuarii
NCBI taxonomy ID ncbi_taxonomy_id	453582
Host organism host_organism	Escherichia coli MC1061

Entity 3 Entity 3 polymer

Description description	Formate dehydrogenase alpha subunit
Molecular weight formula_weight	103751.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKDLIIPPLDWTQDMGTPARHGAPVTLTVDGVEVTVPAGTSVLRAAAQAGISIPKLCATDSVEPVGSCRLCMVEIEGMRGMPSSCTTPVAAGMQVHTQTPQLQKLRRGVMELYISDHPLDCLTCAANGDCELQDMAGAVGLREVRYTKGENHFEVRQGGEANPCYIPKDTSNPYFSYDPAKCIVCMRCVRACEEVQGTFALTVDGRGFEARISPAADNFLASDCVSCGACVQACPTATLVEKSVEEIGTPERKVVTTCAYCGVGCSFEAHMRGEELVRMVPWKGGAANRGHSCVKGRFAYGYATHRDRILKPMIREKVSDPWREVSWEEALGFTAARLNAARATHGADALGVITSSRCTNEETYLVQKLARAVFGTNNTDTCARVCHSPTGYGLKQTFGTSAGTQDFDSVEDTDLALVIGANPTDGHPVFASRLRKRLRAGAKLIVVDPRRIDLLETPHIGDSWHLPLRPGTNVAVLVALAHVIVTEKLYDAAFISERCDGDEWADYAEFVSNPEYAPEAVESLTGVPADTLREAARAYAAAPNAAIYYGLGVTEHSQGSTTVIAIANLAMMTGNIGRPGVGVNPLRGQNNVQGSCDMGSFPHELPGYRHVADDAARSLFEKAWGVALSSEPGLRIPNMLDAAVAGQFKALYVQGEDILQSDPDTRHVAAGLAAMDLVIVHDLFLNETANYAHVFLPGSSFLEKDGTFTNAERRINRVRRVMRPKNGYADWEVTQLLANALGAGWAYTHPREIMAEIAATTPGFANVTYEMLDARGSVQWPCNEAAPEGSPIMHVDGFVRGKGRFIRTAYLPTDERTGPRFPLLLTTGRILSQYNVGAQTRRTENVAWHAEDRLEIHPTDAENRGIREGDWVRVASRAGETTLRATVTDRVSPGVVYTTFHHPDTQANVVTTDNSDWATNCPEYKVTAVQVAPSNGPSAWQEDYTAQATAARRIEAA

Source Source

Source organism organism	Rhodobacter aestuarii
NCBI taxonomy ID ncbi_taxonomy_id	453582
Host organism host_organism	Escherichia coli MC1061

Entity 4 Entity 4 polymer

Description description	Formate dehydrogenase beta subunit
Molecular weight formula_weight	52942.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKIWVPCDAAAKACGAERVVAEITAQAAARGVSVDIRRNGTRGMVWLEPLVEVETEAGRVGFGPMTPADVPALFEDLAAHPKALGLVEEIPFFKRQTRLTFARCGRNEPLCLDQYETTGGWDGLRKALAMTPAEVVEEIISSGLRGRGGAGFPTGIKWRTVLGAAADQKYIVCNVDEGDSGSFADRMLIEGDPFCLIEGMAVAGHAVGATRGYVYIRSEYPDCISVMRAAIILAEQSGILAEAGFSLEVRVGAGAYVCGEETAMLNSIEGKRGTVRPKPPLPALEGLFGKPTVVNNLLSLAAVPWILAHGGAAYQSYGIDRSRGTIPLQVGGNVKYGGLFETGFGITLGELVMDVCGGTASGRPVKAVQVGGPLGAYHPQADFDLPFCYELFAGQGGLVGHAGLVVHDDRADMLKLARFAMEFCAVESCGTCTPCRIGAVRGVETLDRIAAGDAAALPLLDDLCDTMKYGSLCALGGFTPYPVQSAIRHFPQDFPVLREAA

Source Source

Source organism organism	Rhodobacter aestuarii
NCBI taxonomy ID ncbi_taxonomy_id	453582
Host organism host_organism	Escherichia coli MC1061

Entity 5 Entity 5 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
Molecular weight formula_weight	740.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	MOLYBDENUM(VI) ION
Molecular weight formula_weight	95.9 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	10

Entity 9 Entity 9 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

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

Resolution resolution	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	192652

Cryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH

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

Formate dehydrogenase delta 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

Formate dehydrogenase gamma 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

Formate dehydrogenase alpha 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

Formate dehydrogenase beta 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9wxb__assembly_1__model_1

9wxb__assembly_1__model_1 | I(q)

9wxb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

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

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

7. Citations (1)