SAXSdb — 7vmc

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

Elongation factor Tu

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	tRNA nuclease CdiA × 1 （B3BM48） Contact-dependent inhibitor I × 1 （A0A2A3ULE6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E2QJ06_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 1–394

tRNA nuclease CdiA

Escherichia coli O157:H7 (strain EC869)

UniProt B3BM48

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Elongation factor Tu × 1 （E2QJ06） Contact-dependent inhibitor I × 1 （A0A2A3ULE6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDIA1_ECO5C
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 22–306； UniProt 2925–3209

Contact-dependent inhibitor I

Escherichia coli O157:H7 (strain EC869)

UniProt A0A2A3ULE6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Elongation factor Tu × 1 （E2QJ06） tRNA nuclease CdiA × 1 （B3BM48）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2A3ULE6_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–179； UniProt 1–179

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	7vmc
Deposition date deposition_date	2021-10-08
Structure title title	Crystal structure of EF-Tu/CdiA/CdiI
Keywords keywords	Contact-dependent growth inhibition, TOXIN, elongation factor; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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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.

7vmc__assembly_1__model_1

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

Download this curve (.dat)

7vmc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7vmc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.60 Å
Rg (electron density)	32.53 Å
Total Rg	32.95 Å
Atom count	5190
Residues	672
Excluded volume	92683 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7vmc__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Elongation factor Tu
Molecular weight formula_weight	44441.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5190

MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLSLEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	tRNA nuclease CdiA
Molecular weight formula_weight	32256.4 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSSGLVPRGSHMVENNYLSKAQKAQKADELAKCQTAACKAQTEAKWTAIDLGQDGSFAAGMIAGVPAGLYDAVDSIVKAGSNPTETLEAMKALFNSGDILGSLSDAVKQSYIDRIDRMEAEYQKAGTSGSFNAGVEGGKLITDIAGLLAGGVGVVKGGAVLTEKVVAKVVGKSESAAAKVGTDIVKTGTVFDSIKATQPAIPGTSIPKSFELHVNGQTVWVNPNATKHMGEYLTRNGLSHSTAEGSQAMLTSLQSAVKDAFSQGLKFNEKMQVGRWELVFSQRSSDPYPVLKHALYK

Source Source

Source organism organism	Escherichia coli O157:H7 (strain EC869)
NCBI taxonomy ID ncbi_taxonomy_id	478008
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Contact-dependent inhibitor I
Molecular weight formula_weight	19802.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKLTVDSVINEPRSVAITIDGYIPVDIKIIDSKKLPPLYWRGGDGKKNLLELAVLPENGFLSSITLVMIASDSIHKTDSLSVSLPSSECGVPVVNTKLWSHSESDDFSRRFVDDFSLDIEVIISSESMLLTIGENKKVTSWIKCSDNFYLGIDAGRNVVHLYLDKLTPSEVESFFEAVG

Source Source

Source organism organism	Escherichia coli O157:H7 (strain EC869)
NCBI taxonomy ID ncbi_taxonomy_id	478008
Host organism host_organism	Escherichia coli BL21(DE3)

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Unit-cell length a length_a	101.930 Å
Unit-cell length b length_b	102.760 Å
Unit-cell length c length_c	88.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.413 Å
Low-resolution limit resolution_low	35.603 Å
R factor r_factor	0.2386
R_work r_work	0.2368
R_free r_free	0.2735

Crystal structure of EF-Tu/CdiA/CdiI

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

Elongation factor Tu

State in the Current Structure

Other States of the Same Protein in the Database

tRNA nuclease CdiA

State in the Current Structure

Other States of the Same Protein in the Database

Contact-dependent inhibitor I

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

7vmc__assembly_1__model_1

7vmc__assembly_1__model_1 | I(q)

7vmc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)

Crystal structure of EF-Tu/CdiA/CdiI

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

Elongation factor Tu

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

tRNA nuclease CdiA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Contact-dependent inhibitor I

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

7vmc__assembly_1__model_1

7vmc__assembly_1__model_1 | I(q)

7vmc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

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

7. Citations (1)