7bto

EcoR124I-ArdA in the Translocation State

Method: ELECTRON MICROSCOPY

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

Type I restriction enzyme EcoR124II M protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Antirestriction protein ArdA × 2 （A0A0M2A928） Type I restriction enzyme R Protein × 4 （Q304R3） Type-1 restriction enzyme EcoR124II specificity protein × 1 （P10485）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T1M1_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–520； UniProt 1–520 Author chain B； PDBConstruct 1–520； UniProt 1–520

Antirestriction protein ArdA

Enterococcus faecalis EnGen0302

UniProt A0A0M2A928

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Type I restriction enzyme EcoR124II M protein × 2 （P10484） Type I restriction enzyme R Protein × 4 （Q304R3） Type-1 restriction enzyme EcoR124II specificity protein × 1 （P10485）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0M2A928_ENTFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–165； UniProt 1–165 Author chain E； PDBConstruct 1–165； UniProt 1–165

Type I restriction enzyme R Protein

Escherichia coli

UniProt Q304R3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Type I restriction enzyme EcoR124II M protein × 2 （P10484） Antirestriction protein ArdA × 2 （A0A0M2A928） Type-1 restriction enzyme EcoR124II specificity protein × 1 （P10485）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q304R3_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–1038； UniProt 1–1038 Author chain F； PDBConstruct 1–1038； UniProt 1–1038 Author chain G； PDBConstruct 1–1038； UniProt 1–1038 Author chain H； PDBConstruct 1–1038； UniProt 1–1038

Type-1 restriction enzyme EcoR124II specificity protein

Escherichia coli

UniProt P10485

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Type I restriction enzyme EcoR124II M protein × 2 （P10484） Antirestriction protein ArdA × 2 （A0A0M2A928） Type I restriction enzyme R Protein × 4 （Q304R3）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T1S1_ECOLX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain I； PDBConstruct 1–404； UniProt 1–404

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	7bto
Deposition date deposition_date	2020-04-02
Structure title title	EcoR124I-ArdA in the Translocation State
Keywords keywords	Cryoelectron microscopy, Innate immune mechanism, Complex, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

7bto__assembly_1__model_1

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

Download this curve (.dat)

7bto__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7bto__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.16 Å
Rg (electron density)	47.61 Å
Total Rg	47.96 Å
Atom count	21283
Residues	2644
Excluded volume	378810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7bto__assembly_1__model_1`	nonameric （9）	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 (4)

Entity 1 Entity 1 polymer

Description description	Type I restriction enzyme EcoR124II M protein
Molecular weight formula_weight	58077.1 kDa
EC 编号 ec_number	2.1.1.72
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	21283

MKMTSIQQRAELHRQIWQIANDVRGSVDGWDFKQYVLGALFYRFISENFSSYIEAGDDSICYAKLDDSVITDDIKDDAIKTKGYFIYPSQLFCNVAAKANTNDRLNADLNSIFVAIESSAYGYPSEADIKGLFADFDTTSNRLGNTVKDKNARLAAVLKGVEGLKLGDFNEHQIDLFGDAYEFLISNYAANAGKSGGEFFTPQHVSKLIAQLAMHGQTHVNKIYDPAAGSGSLLLQAKKQFDNHIIEEGFFGQEINHTTYNLARMNMFLHNINYDKFDIKLGNTLTEPHFRDEKPFDAIVSNPPYSVKWIGSDDPTLINDERFAPAGVLAPKSKADFAFVLHALNYLSAKGRAAIVCFPGIFYRGGAEQKIRQYLVDNNYVETVISLAPNLFFGTTIAVNILVLSKHKTDTNVQFIDASELFKKETNNNILTDAHIEQIMQVFASKEDVAHLAKSVAFETVVANDYNLSVSSYVEAKDNREIIDIAELNAELKTTVSKIDQLRKDIDAIVAEIEGCEVQK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Antirestriction protein ArdA
Molecular weight formula_weight	19135.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDDMQVYIANLGKYNEGELVGAWFTFPIDFEEVKEKIGLNDEYEEYAIHDYELPFTVDEYTSIGELNRLWEMVSELPEELQSELSALLTHFSSIEELSEHQEDIIIHSDCDDMYDVARYYIEETGALGEVPASLQNYIDYQAYGRDLDLSGTFISTNHGIFEIVY

Source Source

Source organism organism	Enterococcus faecalis EnGen0302
NCBI taxonomy ID ncbi_taxonomy_id	1158660
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Type I restriction enzyme R Protein
Molecular weight formula_weight	120278.9 kDa
EC 编号 ec_number	3.1.21.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,C,H

MTHQTHTIAESNNFIVLDKYIKAEPTGDSYQSESDLERELIQDLRNQGYEFISVKSQSAMLANVREQLQNLNGVVFNDSEWRRFTEQYLDNPSDGILDKTRKIHIDYICDFIFDDERLENIYLIDKKNLMRNKVQIIQQFEQAGSHANRYDVTILVNGLPLVQIELKKRGVAIREAFNQIHRYSKESFNSENSLFKYLQLFVISNGTDTRYFANTTKRDKNSFDFTMNWAKSDNTLIKDLKDFTATCFQKHTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVDRKDLDYQTMKEYQRFSPDSVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFGEAQKNLKKKFKRYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVRPQFKSLETETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTLNTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDLERSTIDAITLFGDKNTKNVVLEKSYTEYMEGFTDAATGEAKRGFMTVVSELEQRFPDPTSIESEKEKKDFVKLFGEYLRAENILQNYDEFATLKALQQIDLSDPVAVEKFKAEHYVDDEKFAELQTIRLPADRKIQDYRSAYNDIRDWQRREKEAEKKEKSTTDWDDVVFEVDLLKSQEINLDYILGLIFEHNRQNKGKGEMIEEVKRLIRSSLGNRAKEGLVVDFIQQTNLDDLPDKASIIDAFFTFAQREQQREAEALIKEENLNEDAAKRYIRTSLKREYATENGTELNETLPKLSPLNPQYKTKKQAVFQKIVSFIEKFKGVGGKI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Type-1 restriction enzyme EcoR124II specificity protein
Molecular weight formula_weight	46235.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MSEMSYLEKLLDGVEVEWLPLGEITKYEQPTKYLVKAKDYHDTYTIPVLTAGKTFILGYTNETHGIYQASKAPVIIFDDFTTANKWVDFDFKAKSSAMKMVTSCDDNKTLLKYVYYWLNTLPSEFAEGDHKRQWISNYSQKKIPIPCPDNPEKSLAIQSEIVRILDKFTALTAELTAELNMRKKQYNYYRDQLLSFKEGEVEWKTLGEIGKWYGGGTPSKNKIEFWENGSIPWISPKDMGRTLVDSSEDYITEEAVLHSSTKLIPANSIAIVVRSSILDKVLPSALIKVPATLNQDMKAVIPHENILVKYIYHMIGSRGSDILRAAKKTGGSVASIDSKKLFSFKIPVPNINEQQRIVEILDKFDTLTNSITEGLPREIELRQKQYEYYRDLLFSFPKPETVSN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id	7btoA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	30 — N6 adenine-specific DNA methyltransferase, N-terminal domain

Domain ID domain_id	7btoA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	7btoB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	7btoD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	480 — Antirestriction protein ArdA, domain 1

Domain ID domain_id	7btoD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	560 — Antirestriction protein ArdA, domain 2

Domain ID domain_id	7btoD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1190 — Antirestriction protein ArdA, domain 3

Domain ID domain_id	7btoE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	480 — Antirestriction protein ArdA, domain 1

Domain ID domain_id	7btoE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	560 — Antirestriction protein ArdA, domain 2

Domain ID domain_id	7btoE03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1190 — Antirestriction protein ArdA, domain 3

Domain ID domain_id	7btoF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7btoG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7btoI01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — DNA methylase specificity domains

Domain ID domain_id	7btoI02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — DNA methylase specificity domains

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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	3.97 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	268962

EcoR124I-ArdA in the Translocation State

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

Type I restriction enzyme EcoR124II M protein

State in the Current Structure

Other States of the Same Protein in the Database

Antirestriction protein ArdA

State in the Current Structure

Other States of the Same Protein in the Database

Type I restriction enzyme R Protein

State in the Current Structure

Other States of the Same Protein in the Database

Type-1 restriction enzyme EcoR124II specificity 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

7bto__assembly_1__model_1

7bto__assembly_1__model_1 | I(q)

7bto__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 (4)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)

EcoR124I-ArdA in the Translocation State

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

Type I restriction enzyme EcoR124II M 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

Antirestriction protein ArdA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Type I restriction enzyme R 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

Type-1 restriction enzyme EcoR124II specificity 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

7bto__assembly_1__model_1

7bto__assembly_1__model_1 | I(q)

7bto__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 (4)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)