SAXSdb — 9y9c

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

Gp77

Escherichia phage SECphi27

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 48	DUF4145 domain-containing protein × 24 （A0A0F3V1L6） ZINC ION × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAE8YXX1_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain IA； PDBConstruct 1–217； UniProt 1–217 Author chain IB； PDBConstruct 1–217； UniProt 1–217 Author chain IC； PDBConstruct 1–217； UniProt 1–217 Author chain ID； PDBConstruct 1–217； UniProt 1–217 Author chain IE； PDBConstruct 1–217； UniProt 1–217 Author chain IF； PDBConstruct 1–217； UniProt 1–217 Author chain IG； PDBConstruct 1–217； UniProt 1–217 Author chain IH； PDBConstruct 1–217； UniProt 1–217 Author chain II； PDBConstruct 1–217； UniProt 1–217 Author chain IJ； PDBConstruct 1–217； UniProt 1–217 Author chain IK； PDBConstruct 1–217； UniProt 1–217 Author chain IL； PDBConstruct 1–217； UniProt 1–217 Author chain IM； PDBConstruct 1–217； UniProt 1–217 Author chain IN； PDBConstruct 1–217； UniProt 1–217 Author chain IO； PDBConstruct 1–217； UniProt 1–217 Author chain IP； PDBConstruct 1–217； UniProt 1–217 Author chain IQ； PDBConstruct 1–217； UniProt 1–217 Author chain IR； PDBConstruct 1–217； UniProt 1–217 Author chain IS； PDBConstruct 1–217； UniProt 1–217 Author chain IT； PDBConstruct 1–217； UniProt 1–217 Author chain IU； PDBConstruct 1–217； UniProt 1–217 Author chain IV； PDBConstruct 1–217； UniProt 1–217 Author chain IW； PDBConstruct 1–217； UniProt 1–217 Author chain IX； PDBConstruct 1–217； UniProt 1–217

DUF4145 domain-containing protein

Escherichia coli

UniProt A0A0F3V1L6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 48	Gp77 × 24 （A0AAE8YXX1） ZINC ION × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0F3V1L6_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain OA； PDBConstruct 1–219； UniProt 1–219 Author chain OB； PDBConstruct 1–219； UniProt 1–219 Author chain OC； PDBConstruct 1–219； UniProt 1–219 Author chain OD； PDBConstruct 1–219； UniProt 1–219 Author chain OE； PDBConstruct 1–219； UniProt 1–219 Author chain OF； PDBConstruct 1–219； UniProt 1–219 Author chain OG； PDBConstruct 1–219； UniProt 1–219 Author chain OH； PDBConstruct 1–219； UniProt 1–219 Author chain OI； PDBConstruct 1–219； UniProt 1–219 Author chain OJ； PDBConstruct 1–219； UniProt 1–219 Author chain OK； PDBConstruct 1–219； UniProt 1–219 Author chain OL； PDBConstruct 1–219； UniProt 1–219 Author chain OM； PDBConstruct 1–219； UniProt 1–219 Author chain ON； PDBConstruct 1–219； UniProt 1–219 Author chain OO； PDBConstruct 1–219； UniProt 1–219 Author chain OP； PDBConstruct 1–219； UniProt 1–219 Author chain OQ； PDBConstruct 1–219； UniProt 1–219 Author chain OR； PDBConstruct 1–219； UniProt 1–219 Author chain OS； PDBConstruct 1–219； UniProt 1–219 Author chain OT； PDBConstruct 1–219； UniProt 1–219 Author chain OU； PDBConstruct 1–219； UniProt 1–219 Author chain OV； PDBConstruct 1–219； UniProt 1–219 Author chain OW； PDBConstruct 1–219； UniProt 1–219 Author chain OX； PDBConstruct 1–219； UniProt 1–219

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	9y9c
Deposition date deposition_date	2025-09-14
Structure title title	Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.
Keywords keywords	Phage-bacterial defense complex, Abortive infection Ring-Activated Zinc-Finger RNase (RAZR), RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

9y9c__assembly_1__model_1

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

Download this curve (.dat)

9y9c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9y9c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	98.05 Å
Rg (electron density)	97.78 Å
Total Rg	98.09 Å
Atom count	112779
Residues	7248
Excluded volume	1008600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9y9c__assembly_1__model_1`	48-meric （48）	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	Gp77
Molecular weight formula_weight	25475.7 kDa
Source method src_method	man
Copy count entity_count	24

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	IA,IB,IC,ID,IE,IF,IG,IH,II,IJ,IK,IL,IM,IN,IO,IP,IQ,IR,IS,IT,IU,IV,IW,IX
Atom count atom_count	112779

MKLSDQFDKVLPALHKARSLFVKVKKDRQNSHLKNRYATLDSVLDAITPALMDNELMIMQDGERIDVSTLRVETTVMHVSGQWVKFYFDIPIVKNDPQGVGSAFTYGRRYSAAAAFGLSQADDDAQIAVKTVNDWKRDIEKCESVGELQEVLKNAWKSSDAASKQVIRDHYEKRKAEIEIGGARGFNPAKPKENLASDAVDTPNSEKVKSQSITDFEGSSGHHHHHH

Source Source

Source organism organism	Escherichia phage SECphi27
NCBI taxonomy ID ncbi_taxonomy_id	2496550
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DUF4145 domain-containing protein
Molecular weight formula_weight	24707.0 kDa
Source method src_method	man
Copy count entity_count	24

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	OA,OB,OC,OD,OE,OF,OG,OH,OI,OJ,OK,OL,OM,ON,OO,OP,OQ,OR,OS,OT,OU,OV,OW,OX

MAEYYPAVFEAEAFNCPHCGVYARQFWRRMYGSARELAQRTTEFRMSTCSHCGDDAYWYDGNMIIPAAGNVELPNPDMPDNCKSDYMEARSIINLSPKGAAALLRLCLQKLMVHLGEPGENINKDIRSLVQKGLPVRIQQAADICRIVGNQAVHPGEISLDDDPQLAHGLFKLLNIIVDDRITRPKEIEAMFQSMPEGPRQGIENQDRQAREQQQAANE

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	24

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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	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	28191

Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.

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

Gp77

State in the Current Structure

Other States of the Same Protein in the Database

DUF4145 domain-containing 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

9y9c__assembly_1__model_1

9y9c__assembly_1__model_1 | I(q)

9y9c__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)

Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.

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

Gp77

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DUF4145 domain-containing 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

9y9c__assembly_1__model_1

9y9c__assembly_1__model_1 | I(q)

9y9c__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)