1jch

Crystal Structure of Colicin E3 in Complex with its Immunity Protein

Method: X-RAY DIFFRACTION

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

COLICIN E3

Escherichia coli str. K12 substr.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	COLICIN E3 IMMUNITY PROTEIN × 2 （P02984） CITRIC ACID × 4 GLYCEROL × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	COLICIN E3 IMMUNITY PROTEIN × 1 （P02984） CITRIC ACID × 2 GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	COLICIN E3 IMMUNITY PROTEIN × 1 （P02984） CITRIC ACID × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CEA3_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–551； UniProt 1–551 Author chain C； PDBConstruct 1–551； UniProt 1–551

COLICIN E3 IMMUNITY PROTEIN

Escherichia coli str. K12 substr.

UniProt P02984

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	COLICIN E3 × 2 （P00646） CITRIC ACID × 4 GLYCEROL × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	COLICIN E3 × 1 （P00646） CITRIC ACID × 2 GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	COLICIN E3 × 1 （P00646） CITRIC ACID × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IMM3_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–84； UniProt 1–84 Author chain D； PDBConstruct 1–84； UniProt 1–84

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	1jch
Deposition date deposition_date	2001-06-09
Structure title title	Crystal Structure of Colicin E3 in Complex with its Immunity Protein
Keywords keywords	;TRANSLOCATION DOMAIN IS A BETA-JELLYROLL, THE RECEPTOR-BINDING DOMAIN IS A COILED COIL, THE RNASE DOMAIN IS A SIX-STRANDED ANTIPARALLEL BETA-SHEET. THE IMMUNITY PROTEIN IS A FOUR-STRANDED ANTIPARALLEL BETA SHEET FLANKED BY 3 HELICES ON ONE SIDE OF THE SHEET, RIBOSOME INHIBITOR, HYDROLASE ;; RIBOSOME INHIBITOR, HYDROLASE
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.

1jch__assembly_1__model_1

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

Download this curve (.dat)

1jch__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jch__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.78 Å
Rg (electron density)	62.60 Å
Total Rg	62.06 Å
Atom count	8602
Residues	1104
Excluded volume	150800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jch__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jch__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1jch__assembly_3__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	COLICIN E3
Molecular weight formula_weight	58043.0 kDa
EC 编号 ec_number	3.1.21.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8998

MSGGDGRGHNTGAHSTSGNINGGPTGLGVGGGASDGSGWSSENNPWGGGSGSGIHWGGGSGHGNGGGNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGPFKFGLWGVALYGVLPSQIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATVNVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNNSTPAVQTLSPGVTNNTDKDVRPAFGTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQRQDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKNKPRKGFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL

Source Source

Source organism organism	Escherichia coli str. K12 substr.
NCBI taxonomy ID ncbi_taxonomy_id	316407
Host organism host_organism	Escherichia coli str. K12 substr. W3110

Entity 2 Entity 2 polymer

Description description	COLICIN E3 IMMUNITY PROTEIN
Molecular weight formula_weight	9779.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW

Source Source

Source organism organism	Escherichia coli str. K12 substr.
NCBI taxonomy ID ncbi_taxonomy_id	316407
Host organism host_organism	Escherichia coli str. K12 substr. W3110

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	396

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1jcha1
Class class	b — All beta proteins
Fold Fold fold	b.101 — Ribonuclease domain of colicin E3
Superfamily Superfamily superfamily	b.101.1 — Ribonuclease domain of colicin E3
Family Family family	b.101.1.1 — Ribonuclease domain of colicin E3

Domain ID domain_id	d1jcha2
Class class	b — All beta proteins
Fold Fold fold	b.110 — Cloacin translocation domain
Superfamily Superfamily superfamily	b.110.1 — Cloacin translocation domain
Family Family family	b.110.1.1 — Cloacin translocation domain

Domain ID domain_id	d1jcha3
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.9 — Colicin E3 receptor domain
Family Family family	h.4.9.1 — Colicin E3 receptor domain

Domain ID domain_id	d1jchb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.2 — Colicin E3 immunity protein
Family Family family	d.26.2.1 — Colicin E3 immunity protein

Domain ID domain_id	d1jchc1
Class class	b — All beta proteins
Fold Fold fold	b.101 — Ribonuclease domain of colicin E3
Superfamily Superfamily superfamily	b.101.1 — Ribonuclease domain of colicin E3
Family Family family	b.101.1.1 — Ribonuclease domain of colicin E3

Domain ID domain_id	d1jchc2
Class class	b — All beta proteins
Fold Fold fold	b.110 — Cloacin translocation domain
Superfamily Superfamily superfamily	b.110.1 — Cloacin translocation domain
Family Family family	b.110.1.1 — Cloacin translocation domain

Domain ID domain_id	d1jchc3
Class class	h — Coiled coil proteins
Fold Fold fold	h.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamily	h.4.9 — Colicin E3 receptor domain
Family Family family	h.4.9.1 — Colicin E3 receptor domain

Domain ID domain_id	d1jchd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.2 — Colicin E3 immunity protein
Family Family family	d.26.2.1 — Colicin E3 immunity protein

CATH v4.4 (6 domains)

Domain ID domain_id	1jchA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	620 — Helix Hairpins

Domain ID domain_id	1jchA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	380 — Ribonuclease domain of colicin e3 (Residues 456-551)
Homologous superfamily homologous superfamily	10 — Colicin E3-like ribonuclease domain

Domain ID domain_id	1jchB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	20 — Cloacin immunity protein

Domain ID domain_id	1jchC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	620 — Helix Hairpins

Domain ID domain_id	1jchC03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	380 — Ribonuclease domain of colicin e3 (Residues 456-551)
Homologous superfamily homologous superfamily	10 — Colicin E3-like ribonuclease domain

Domain ID domain_id	1jchD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	20 — Cloacin immunity protein

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Unit-cell length a length_a	66.986 Å
Unit-cell length b length_b	195.733 Å
Unit-cell length c length_c	85.124 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.020 Å
Low-resolution limit resolution_low	20.170 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2830

Crystal Structure of Colicin E3 in Complex with its Immunity Protein

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

COLICIN E3

State in the Current Structure

Other States of the Same Protein in the Database

COLICIN E3 IMMUNITY PROTEIN

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

1jch__assembly_1__model_1

1jch__assembly_1__model_1 | I(q)

1jch__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Colicin E3 in Complex with its Immunity Protein

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

COLICIN E3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

COLICIN E3 IMMUNITY PROTEIN

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

1jch__assembly_1__model_1

1jch__assembly_1__model_1 | I(q)

1jch__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)