9O8U | pdb_00009o8u

(1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex with bound fumarate

PDB DOI: https://doi.org/10.2210/pdb9O8U/pdb
EM Map EMD-70238: EMDB EMDataResource

Classification: LYASE
Organism(s): Azoarcus sp. HxN1
Expression System: Escherichia coli #1/H766, Escherichia, Escherichia coli
Mutation(s): No

Deposited: 2025-04-16 Released: 2025-07-23
Deposition Author(s): Andorfer, M.C., Drennan, C.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural Basis for Anaerobic Alkane Activation by a Multi-Subunit Glycyl Radical Enzyme

Andorfer, M.C., Drennan, C.L.

To be published.

Macromolecule Content

Total Structure Weight: 230.77 kDa
Atom Count: 13,972
Modeled Residue Count: 1,746
Deposited Residue Count: 2,027
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-methyl alkyl succinate synthase subunit MasD	A, E	858	Azoarcus sp. HxN1	Mutation(s): 0 Gene Names: masD
UniProt
Find proteins for A9J4K4 (Azoarcus sp. HxN1) Explore A9J4K4 Go to UniProtKB: A9J4K4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9J4K4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MasB protein	B	120	Azoarcus sp. HxN1	Mutation(s): 0 Gene Names: masB
UniProt
Find proteins for A9J4K0 (Azoarcus sp. HxN1) Explore A9J4K0 Go to UniProtKB: A9J4K0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9J4K0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1-methyl alkyl succinate synthase subunit MasC	C, F	60	Azoarcus sp. HxN1	Mutation(s): 0 Gene Names: masC
UniProt
Find proteins for A9J4K2 (Azoarcus sp. HxN1) Explore A9J4K2 Go to UniProtKB: A9J4K2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9J4K2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
1-methyl alkyl succinate synthase subunit Mas E	D	71	Azoarcus sp. HxN1	Mutation(s): 0 Gene Names: masE
UniProt
Find proteins for A9J4K6 (Azoarcus sp. HxN1) Explore A9J4K6 Go to UniProtKB: A9J4K6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9J4K6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain L [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth F] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth F]	I [auth B], J [auth C], L [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth F]
DTT (Subject of Investigation/LOI) Query on DTT Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
FUM (Subject of Investigation/LOI) Query on FUM Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	FUMARIC ACID C₄ H₄ O₄ VZCYOOQTPOCHFL-OWOJBTEDSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Andorfer, M.C.

Drennan, C.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM129882
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM145910