7z0s

Structure of the Escherichia coli formate hydrogenlyase complex (anaerobic preparation, without formate dehydrogenase H)

Method: ELECTRON MICROSCOPY

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

Formate hydrogenlyase subunit 3

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Formate hydrogenlyase subunit 5 × 1 （P16431） Formate hydrogenlyase subunit 2 × 1 （P0AAK1） Formate hydrogenlyase subunit 7 × 1 （P16433） Formate hydrogenlyase subunit 6 × 1 （P16432） Formate hydrogenlyase subunit 4 × 1 （P16430） CARDIOLIPIN × 1 PHOSPHATIDYLETHANOLAMINE × 2 NICKEL (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL × 1 IRON/SULFUR CLUSTER × 7 FE (III) ION × 1 Lauryl Maltose Neopentyl Glycol × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYCC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–608； UniProt 1–608

Formate hydrogenlyase subunit 5

Escherichia coli K-12

UniProt P16431

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Formate hydrogenlyase subunit 3 × 1 （P16429） Formate hydrogenlyase subunit 2 × 1 （P0AAK1） Formate hydrogenlyase subunit 7 × 1 （P16433） Formate hydrogenlyase subunit 6 × 1 （P16432） Formate hydrogenlyase subunit 4 × 1 （P16430） CARDIOLIPIN × 1 PHOSPHATIDYLETHANOLAMINE × 2 NICKEL (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL × 1 IRON/SULFUR CLUSTER × 7 FE (III) ION × 1 Lauryl Maltose Neopentyl Glycol × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYCE_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–83； UniProt 1–83 Author chain E； PDBConstruct 96–581； UniProt 84–569

Formate hydrogenlyase subunit 2

OrganismNot specified

UniProt P0AAK1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Formate hydrogenlyase subunit 3 × 1 （P16429） Formate hydrogenlyase subunit 5 × 1 （P16431） Formate hydrogenlyase subunit 7 × 1 （P16433） Formate hydrogenlyase subunit 6 × 1 （P16432） Formate hydrogenlyase subunit 4 × 1 （P16430） CARDIOLIPIN × 1 PHOSPHATIDYLETHANOLAMINE × 2 NICKEL (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL × 1 IRON/SULFUR CLUSTER × 7 FE (III) ION × 1 Lauryl Maltose Neopentyl Glycol × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYCB_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–203； UniProt 1–203

Formate hydrogenlyase subunit 7

OrganismNot specified

UniProt P16433

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Formate hydrogenlyase subunit 3 × 1 （P16429） Formate hydrogenlyase subunit 5 × 1 （P16431） Formate hydrogenlyase subunit 2 × 1 （P0AAK1） Formate hydrogenlyase subunit 6 × 1 （P16432） Formate hydrogenlyase subunit 4 × 1 （P16430） CARDIOLIPIN × 1 PHOSPHATIDYLETHANOLAMINE × 2 NICKEL (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL × 1 IRON/SULFUR CLUSTER × 7 FE (III) ION × 1 Lauryl Maltose Neopentyl Glycol × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYCG_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 1–255； UniProt 1–255

Formate hydrogenlyase subunit 6

OrganismNot specified

UniProt P16432

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Formate hydrogenlyase subunit 3 × 1 （P16429） Formate hydrogenlyase subunit 5 × 1 （P16431） Formate hydrogenlyase subunit 2 × 1 （P0AAK1） Formate hydrogenlyase subunit 7 × 1 （P16433） Formate hydrogenlyase subunit 4 × 1 （P16430） CARDIOLIPIN × 1 PHOSPHATIDYLETHANOLAMINE × 2 NICKEL (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL × 1 IRON/SULFUR CLUSTER × 7 FE (III) ION × 1 Lauryl Maltose Neopentyl Glycol × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYCF_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–180； UniProt 1–180

Formate hydrogenlyase subunit 4

OrganismNot specified

UniProt P16430

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Formate hydrogenlyase subunit 3 × 1 （P16429） Formate hydrogenlyase subunit 5 × 1 （P16431） Formate hydrogenlyase subunit 2 × 1 （P0AAK1） Formate hydrogenlyase subunit 7 × 1 （P16433） Formate hydrogenlyase subunit 6 × 1 （P16432） CARDIOLIPIN × 1 PHOSPHATIDYLETHANOLAMINE × 2 NICKEL (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL × 1 IRON/SULFUR CLUSTER × 7 FE (III) ION × 1 Lauryl Maltose Neopentyl Glycol × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYCD_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–307； UniProt 1–307

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	7z0s
Deposition date deposition_date	2022-02-23
Structure title title	Structure of the Escherichia coli formate hydrogenlyase complex (anaerobic preparation, without formate dehydrogenase H)
Keywords keywords	FHL, group-4 membrane bound hydrogenase, [NiFe] hydrogenase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

7z0s__assembly_1__model_1

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

Download this curve (.dat)

7z0s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7z0s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.17 Å
Rg (electron density)	43.49 Å
Total Rg	44.00 Å
Atom count	15860
Residues	2026
Excluded volume	287530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7z0s__assembly_1__model_1`	hexameric （6）	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 (15)

Entity 1 Entity 1 polymer

Description description	Formate hydrogenlyase subunit 3
Molecular weight formula_weight	64121.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	15969

MSAISLINSGVAWFVAAAVLAFLFSFQKALSGWIAGIGGAVGSLYTAAAGFTVLTGAVGVSGALSLVSYDVQISPLNAIWLITLGLCGLFVSLYNIDWHRHAQVKCNGLQINMLMAAAVCAVIASNLGMFVVMAEIMALCAVFLTSNSKEGKLWFALGRLGTLLLAIACWLLWQRYGTLDLRLLDMRMQQLPLGSDIWLLGVIGFGLLAGIIPLHGWVPQAHANASAPAAALFSTVVMKIGLLGILTLSLLGGNAPLWWGIALLVLGMITAFVGGLYALVEHNIQRLLAYHTLENIGIILLGLGAGVTGIALEQPALIALGLVGGLYHLLNHSLFKSVLFLGAGSVWFRTGHRDIEKLGGIGKKMPVISIAMLVGLMAMAALPPLNGFAGEWVIYQSFFKLSNSGAFVARLLGPLLAVGLAITGALAVMCMAKVYGVTFLGAPRTKEAENATCAPLLMSVSVVALAICCVIGGVAAPWLLPMLSAAVPLPLEPANTTVSQPMITLLLIACPLLPFIIMAICKGDRLPSRSRGAAWVCGYDHEKSMVITAHGFAMPVKQAFAPVLKLRKWLNPVSLVPGWQCEGSALLFRRMALVELAVLVVIIVSRGA

Entity 2 Entity 2 polymer

Description description	Formate hydrogenlyase subunit 5
Molecular weight formula_weight	66589.9 kDa
Mutation mutation	internal deca-His-Gly-Ser sequence after Gly83
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSEEKLGQHYLAALNEAFPGVVLDHAWQTKDQLTVTVKVNYLPEVVEFLYYKQGGWLSVLFGNDERKLNGHYAVYYVLSMEKGHHHHHHHHHHGSTKCWITVRVEVDANKPEYPSVTPRVPAAVWGEREVRDMYGLIPVGLPDERRLVLPDDWPDELYPLRKDSMDYRQRPAPTTDAETYEFINELGDKKNNVVPIGPLHVTSDEPGHFRLFVDGENIIDADYRLFYVHRGMEKLAETRMGYNEVTFLSDRVCGICGFAHSTAYTTSVENAMGIQVPERAQMIRAILLEVERLHSHLLNLGLACHFTGFDSGFMQFFRVRETSMKMAEILTGARKTYGLNLIGGIRRDLLKDDMIQTRQLAQQMRREVQELVDVLLSTPNMEQRTVGIGRLDPEIARDFSNVGPMVRASGHARDTRADHPFVGYGLLPMEVHSEQGCDVISRLKVRINEVYTALNMIDYGLDNLPGGPLMVEGFTYIPHRFALGFAEAPRGDDIHWSMTGDNQKLYRWRCRAATYANWPTLRYMLRGNTVSDAPLIIGSLDPCYSCTDRMTVVDVRKKKSKVVPYKELERYSIERKNSPLK

Source Source

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

Entity 3 Entity 3 polymer

Description description	Formate hydrogenlyase subunit 2
Molecular weight formula_weight	21899.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNRFVIADSTLCIGCHTCEAACSETHRQHGLQSMPRLRVMLNEKESAPQLCHHCEDAPCAVVCPVNAITRVDGAVQLNESLCVSCKLCGIACPFGAIEFSGSRPLDIPANANTPKAPPAPPAPARVSTLLDWVPGIRAIAVKCDLCSFDEQGPACVRMCPTKALHLVDNTDIARVSKRKRELTFNTDFGDLTLFQQAQSGEAK

Entity 4 Entity 4 polymer

Description description	Formate hydrogenlyase subunit 7
Molecular weight formula_weight	28033.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSNLLGPRDANGIPVPMTVDESIASMKASLLKKIKRSAYVYRVDCGGCNGCEIEIFATLSPLFDAERFGIKVVPSPRHADILLFTGAVTRAMRSPALRAWQSAPDPKICISYGACGNSGGIFHDLYCVWGGTDKIVPVDVYIPGCPPTPAATLYGFAMALGLLEQKIHARGPGELDEQPAEILHGDMVQPLRVKVDREARRLAGYRYGRQIADDYLTQLGQGEEQVARWLEAENDPRLNEIVSHLNHVVEEARIR

Entity 5 Entity 5 polymer

Description description	Formate hydrogenlyase subunit 6
Molecular weight formula_weight	20336.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MFTFIKKVIKTGTATSSYPLEPIAVDKNFRGKPEQNPQQCIGCAACVNACPSNALTVETDLATGELAWEFNLGHCIFCGRCEEVCPTAAIKLSQEYELAVWKKEDFLQQSRFALCNCRVCNRPFAVQKEIDYAIALLKHNGDSRAENHRESFETCPECKRQKCLVPSDRIELTRHMKEAI

Entity 6 Entity 6 polymer

Description description	Formate hydrogenlyase subunit 4
Molecular weight formula_weight	33049.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSVLYPLIQALVLFAVAPLLSGITRVARARLHNRRGPGVLQEYRDIIKLLGRQSVGPDASGWVFRLTPYVMVGVMLTIATALPVVTVGSPLPQLGDLITLLYLFAIARFFFAISGLDTGSPFTAIGASREAMLGVLVEPMLLLGLWVAAQVAGSTNISNITDTVYHWPLSQSIPLVLALCACAFATFIEMGKLPFDLAEAEQELQEGPLSEYSGSGFGVMKWGISLKQLVVLQMFVGVFIPWGQMETFTAGGLLLALVIAIVKLVVGVLVIALFENSMARLRLDITPRITWAGFGFAFLAFVSLLAA

Entity 7 Entity 7 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	CARBONMONOXIDE-(DICYANO) IRON
Molecular weight formula_weight	135.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
Molecular weight formula_weight	747.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 13 Entity 13 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	Lauryl Maltose Neopentyl Glycol
Molecular weight formula_weight	1005.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7z0sE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	80 — NADH:ubiquinone oxidoreductase Nqo5 subunit

Domain ID domain_id	7z0sE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

Domain ID domain_id	7z0sF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3270 —

Domain ID domain_id	7z0sG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12280 —

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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	2.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	300386

Structure of the Escherichia coli formate hydrogenlyase complex (anaerobic preparation, without formate dehydrogenase H)

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

Formate hydrogenlyase subunit 3

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 hydrogenlyase subunit 5

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 hydrogenlyase subunit 2

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 hydrogenlyase subunit 7

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 hydrogenlyase subunit 6

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 hydrogenlyase subunit 4

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

7z0s__assembly_1__model_1

7z0s__assembly_1__model_1 | I(q)

7z0s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer 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

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer