2vdc

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

Method: ELECTRON MICROSCOPY

▼

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

GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN

AZOSPIRILLUM BRASILENSE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN × 6 （Q05756） S-DIOXYMETHIONINE × 6 FLAVIN MONONUCLEOTIDE × 6 2-OXOGLUTARIC ACID × 6 FE3-S4 CLUSTER × 6 IRON/SULFUR CLUSTER × 12 FLAVIN-ADENINE DINUCLEOTIDE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLTB_AZOBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1472； UniProt 37–1508 Author chain B； PDBConstruct 1–1472； UniProt 37–1508 Author chain C； PDBConstruct 1–1472； UniProt 37–1508 Author chain D； PDBConstruct 1–1472； UniProt 37–1508 Author chain E； PDBConstruct 1–1472； UniProt 37–1508 Author chain F； PDBConstruct 1–1472； UniProt 37–1508

GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN

AZOSPIRILLUM BRASILENSE

UniProt Q05756

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN × 6 （Q05755） S-DIOXYMETHIONINE × 6 FLAVIN MONONUCLEOTIDE × 6 2-OXOGLUTARIC ACID × 6 FE3-S4 CLUSTER × 6 IRON/SULFUR CLUSTER × 12 FLAVIN-ADENINE DINUCLEOTIDE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLTD_AZOBR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–456； UniProt 27–482 Author chain H； PDBConstruct 1–456； UniProt 27–482 Author chain I； PDBConstruct 1–456； UniProt 27–482 Author chain J； PDBConstruct 1–456； UniProt 27–482 Author chain K； PDBConstruct 1–456； UniProt 27–482 Author chain L； PDBConstruct 1–456； UniProt 27–482

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	2vdc
Deposition date deposition_date	2007-10-04
Structure title title	THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.
Keywords keywords	;OXIDOREDUCTASE, AMIDOTRANSFERASE, AMMONIA ASSIMILATION, NADP, IRON, ZYMOGEN, NADPH-DEPENDENT GLUTAMATE SYNTHASE, IRON SULPHUR FLAVOPROTEIN, GLUTAMINE AMIDOTRANSFERASE, GLUTAMATE BIOSYNTHESIS, AMINO-ACID BIOSYNTHESIS ;; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

2vdc__assembly_1__model_1

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

Download this curve (.dat)

2vdc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vdc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	74.35 Å
Rg (electron density)	73.64 Å
Total Rg	73.71 Å
Atom count	89598
Residues	11568
Excluded volume	1587700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vdc__assembly_1__model_1`	dodecameric （12）	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	GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN
Molecular weight formula_weight	161615.9 kDa
EC 编号 ec_number	1.4.1.13
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	89598

CGVGFIAAIDGKPRRSVVEKGIEALKAVWHRGAVDADGKTGDGAGIHVAVPQKFFKDHVKVIGHRAPDNKLAVGQVFLPRISLDAQEACRCIVETEILAFGYYIYGWRQVPINVDIIGEKANATRPEIEQIIVGNNKGVSDEQFELDLYIIRRRIEKAVKGEQINDFYICSLSARSIIYKGMFLAEQLTTFYPDLLDERFESDFAIYHQRYSTNTFPTWPLAQPFRMLAHNGEINTVKGNVNWMKAHETRMEHPAFGTHMQDLKPVIGVGLSDSGSLDTVFEVMVRAGRTAPMVKMMLVPQALTSSQTTPDNHKALIQYCNSVMEPWDGPAALAMTDGRWVVGGMDRNGLRPMRYTITTDGLIIGGSETGMVKIDETQVIEKGRLGPGEMIAVDLQSGKLYRDRELKDHLATLKPWDKWVQNTTHLDELVKTASLKGEPSDMDKAELRRRQQAFGLTMEDMELILHPMVEDGKEAIGSMGDDSPIAVLSDKYRGLHHFFRQNFSQVTNPPIDSLRERRVMSLKTRLGNLGNILDEDETQTRLLQLESPVLTTAEFRAMRDYMGDTAAEIDATFPVDGGPEALRDALRRIRQETEDAVRGGATHVILTDEAMGPARAAIPAILATGAVHTHLIRSNLRTFTSLNVRTAEGLDTHYFAVLIGVGATTVNAYLAQEAIAERHRRGLFGSMPLEKGMANYKKAIDDGLLKIMSKMGISVISSYRGGGNFEAIGLSRALVAEHFPAMVSRISGIGLNGIQKKVLEQHATAYNEEVVALPVGGFYRFRKSGDRHGWEGGVIHTLQQAVTNDSYTTFKKYSEQVNKRPPMQLRDLLELRSTKAPVPVDEVESITAIRKRFITPGMSMGALSPEAHGTLNVAMNRIGAKSDSGEGGEDPARFRPDKNGDNWNSAIKQVASGRFGVTAEYLNQCRELEIKVAQGAKPGEGGQLPGFKVTEMIARLRHSTPGVMLISPPPHHDIYSIEDLAQLIYDLKQINPDAKVTVKLVSRSGIGTIAAGVAKANADIILISGNSGGTGASPQTSIKFAGLPWEMGLSEVHQVLTLNRLRHRVRLRTDGGLKTGRDIVIAAMLGAEEFGIGTASLIAMGCIMVRQCHSNTCPVGVCVQDDKLRQKFVGTPEKVVNLFTFLAEEVREILAGLGFRSLNEVIGRTDLLHQVSRGAEHLDDLDLNPRLAQVDPGENARYCTLQGRNEVPDTLDARIVADARPLFEEGEKMQLAYNARNTQRAIGTRLSSMVTRKFGMFGLQPGHITIRLRGTAGQSLGAFAVQGIKLEVMGDANDYVGKGLSGGTIVVRPTTSSPLETNKNTIIGNTVLYGATAGKLFAAGQAGERFAVRNSGATVVVEGCGSNGCEYMTGGTAVILGRVGDNFAAGMTGGMAYVYDLDDSLPLYINDESVIFQRIEVGHYESQLKHLIEEHVTETQSRFAAEILNDWAREVTKFWQVVPKEMLNRLEVPVHL

Source Source

Source organism organism	AZOSPIRILLUM BRASILENSE
NCBI taxonomy ID ncbi_taxonomy_id	192
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN
Molecular weight formula_weight	49367.5 kDa
EC 编号 ec_number	1.4.1.13
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

QDFAEIYARFSDERANEQANRCSQCGVPFCQVHCPVSNNIPDWLKLTSEGRLEEAYEVSQATNNFPEICGRICPQDRLCEGNCVIEQSTHGAVTIGSVEKYINDTAWDQGWVKPRTPSRELGLSVGVIGAGPAGLAAAEELRAKGYEVHVYDRYDRMGGLLVYGIPGFKLEKSVVERRVKLLADAGVIYHPNFEVGRDASLPELRRKHVAVLVATGVYKARDIKAPGSGLGNIVAALDYLTTSNKVSLGDTVEAYENGSLNAAGKHVVVLGGGDTAMDCVRTAIRQGATSVKCLYRRDRKNMPGSQREVAHAEEEGVEFIWQAAPEGFTGDTVVTGVRAVRIHLGVADATGRQTPQVIEGSEFTVQADLVIKALGFEPEDLPNAFDEPELKVTRWGTLLVDHRTKMTNMDGVFAAGDIVRGASLVVWAIRDGRDAAEGIHAYAKAKAEAPVAVAAE

Source Source

Source organism organism	AZOSPIRILLUM BRASILENSE
NCBI taxonomy ID ncbi_taxonomy_id	192
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	S-DIOXYMETHIONINE
Molecular weight formula_weight	181.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 8 Entity 8 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	6

▼

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d2vdca1
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
Family Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

Domain ID domain_id	d2vdca2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d2vdca3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d2vdcb1
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
Family Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

Domain ID domain_id	d2vdcb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d2vdcb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d2vdcc1
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
Family Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

Domain ID domain_id	d2vdcc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d2vdcc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d2vdcd1
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
Family Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

Domain ID domain_id	d2vdcd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d2vdcd3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d2vdce1
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
Family Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

Domain ID domain_id	d2vdce2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d2vdce3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d2vdcf1
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain
Family Family family	b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain

Domain ID domain_id	d2vdcf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d2vdcf3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

▶

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	1

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

Resolution resolution	9.500 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	9.50 Å
Resolution测定Method resolution_method	;RANDOM CONICAL TILT SERIES (CRYOEM) AND REFINEMENT BY PROJECTION MATCHING AND CTF CORRECTION USING WIENER FILTERING OF VOLUMES FROM FOCAL SERIES ;
颗粒数 num_particles	12800

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

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

GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN

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

2vdc__assembly_1__model_1

2vdc__assembly_1__model_1 | I(q)

2vdc__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-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

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

7. Citations (1)

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

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

GLUTAMATE SYNTHASE [NADPH] LARGE 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

GLUTAMATE SYNTHASE [NADPH] SMALL 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2vdc__assembly_1__model_1

2vdc__assembly_1__model_1 | I(q)

2vdc__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-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

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

7. Citations (1)