8rhp

Cryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII)

Method: ELECTRON MICROSCOPY

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

Nitrogenase molybdenum-iron protein alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nitrogenase molybdenum-iron protein beta chain × 4 （P07329） Protein FeSII × 2 （Q44501） Nitrogenase iron protein 1 × 4 （P00459） FE(8)-S(7) CLUSTER × 4 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 4 iron-sulfur-molybdenum cluster with interstitial carbon × 4 CALCIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 IRON/SULFUR CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIFD_AZOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–492； UniProt 1–492 Author chain D； PDBConstruct 1–492； UniProt 1–492 Author chain H； PDBConstruct 1–492； UniProt 1–492 Author chain K； PDBConstruct 1–492； UniProt 1–492

Nitrogenase molybdenum-iron protein beta chain

OrganismNot specified

UniProt P07329

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nitrogenase molybdenum-iron protein alpha chain × 4 （P07328） Protein FeSII × 2 （Q44501） Nitrogenase iron protein 1 × 4 （P00459） FE(8)-S(7) CLUSTER × 4 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 4 iron-sulfur-molybdenum cluster with interstitial carbon × 4 CALCIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 IRON/SULFUR CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIFK_AZOVI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–523； UniProt 1–523 Author chain C； PDBConstruct 1–523； UniProt 1–523 Author chain I； PDBConstruct 1–523； UniProt 1–523 Author chain J； PDBConstruct 1–523； UniProt 1–523

Protein FeSII

Azotobacter vinelandii

UniProt Q44501

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nitrogenase molybdenum-iron protein alpha chain × 4 （P07328） Nitrogenase molybdenum-iron protein beta chain × 4 （P07329） Nitrogenase iron protein 1 × 4 （P00459） FE(8)-S(7) CLUSTER × 4 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 4 iron-sulfur-molybdenum cluster with interstitial carbon × 4 CALCIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 IRON/SULFUR CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FESII_AZOVI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–122； UniProt 1–122 Author chain L； PDBConstruct 1–122； UniProt 1–122

Nitrogenase iron protein 1

OrganismNot specified

UniProt P00459

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Nitrogenase molybdenum-iron protein alpha chain × 4 （P07328） Nitrogenase molybdenum-iron protein beta chain × 4 （P07329） Protein FeSII × 2 （Q44501） FE(8)-S(7) CLUSTER × 4 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 4 iron-sulfur-molybdenum cluster with interstitial carbon × 4 CALCIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 IRON/SULFUR CLUSTER × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIFH1_AZOVI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–290； UniProt 1–290 Author chain G； PDBConstruct 1–290； UniProt 1–290 Author chain M； PDBConstruct 1–290； UniProt 1–290 Author chain N； PDBConstruct 1–290； UniProt 1–290

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	8rhp
Deposition date deposition_date	2023-12-15
Structure title title	Cryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII)
Keywords keywords	nitrogenase complex, 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.

8rhp__assembly_1__model_1

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

Download this curve (.dat)

8rhp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rhp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	67.90 Å
Rg (electron density)	67.95 Å
Total Rg	67.89 Å
Atom count	42592
Residues	5394
Excluded volume	760090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rhp__assembly_1__model_1`	14-meric （14）	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	Nitrogenase molybdenum-iron protein alpha chain
Molecular weight formula_weight	55363.0 kDa
EC 编号 ec_number	1.18.6.1
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,H,K
Atom count atom_count	42728

MTGMSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWEASEGAEKVAASA

Entity 2 Entity 2 polymer

Description description	Nitrogenase molybdenum-iron protein beta chain
Molecular weight formula_weight	59535.9 kDa
EC 编号 ec_number	1.18.6.1
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,I,J

MSQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

Entity 3 Entity 3 polymer

Description description	Protein FeSII
Molecular weight formula_weight	13289.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MATIYFSSPLMPHNKKVQAVAGKRSTLLGVAQENGVKIPFECQDGNCGSCLVKITHLDGERIKGMLLTDKERNVLKSVGKLPKSEEERAAVRDLPPTYRLACQTIVTDEDLLVEFTGEPGGA

Source Source

Source organism organism	Azotobacter vinelandii
NCBI taxonomy ID ncbi_taxonomy_id	354
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Nitrogenase iron protein 1
Molecular weight formula_weight	31548.2 kDa
EC 编号 ec_number	1.18.6.1
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,M,N

MAMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV

Entity 5 Entity 5 non-polymer

Description description	FE(8)-S(7) CLUSTER
Molecular weight formula_weight	671.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	3-HYDROXY-3-CARBOXY-ADIPIC ACID
Molecular weight formula_weight	206.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	iron-sulfur-molybdenum cluster with interstitial carbon
Molecular weight formula_weight	787.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 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 10 Entity 10 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 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	2.89 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	261829

Cryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII)

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

Nitrogenase molybdenum-iron protein alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Nitrogenase molybdenum-iron protein beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Protein FeSII

State in the Current Structure

Other States of the Same Protein in the Database

Nitrogenase iron protein 1

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

8rhp__assembly_1__model_1

8rhp__assembly_1__model_1 | I(q)

8rhp__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

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)

Cryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII)

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

Nitrogenase molybdenum-iron protein alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrogenase molybdenum-iron protein beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein FeSII

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrogenase iron protein 1

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

8rhp__assembly_1__model_1

8rhp__assembly_1__model_1 | I(q)

8rhp__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

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)