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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 48 PDB declaration: 48-meric（48） Consistent with protein copy count	Chain IA； UniProt 1–217 Chain IB； UniProt 1–217 Chain IC； UniProt 1–217 Chain ID； UniProt 1–217 Chain IE； UniProt 1–217 Chain IF； UniProt 1–217 Chain IG； UniProt 1–217 Chain IH； UniProt 1–217 Chain II； UniProt 1–217 Chain IJ； UniProt 1–217 Chain IK； UniProt 1–217 Chain IL； UniProt 1–217 Chain IM； UniProt 1–217 Chain IN； UniProt 1–217 Chain IO； UniProt 1–217 Chain IP； UniProt 1–217 Chain IQ； UniProt 1–217 Chain IR； UniProt 1–217 Chain IS； UniProt 1–217 Chain IT； UniProt 1–217 Chain IU； UniProt 1–217 Chain IV； UniProt 1–217 Chain IW； UniProt 1–217 Chain IX； UniProt 1–217	Not recorded	DUF4145 domain-containing protein × 24 （A0A0F3V1L6） ZN ZINC ION × 24	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9Y9C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Y6U Cryo-EM Structure of Gp77 within the In Vitro Reconstituted RAZR:GP77 Complex Deposited 2025-09-09	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain IA 1–217（217 aa） Chain IB 1–217（217 aa） Chain IC 1–217（217 aa） Chain ID 1–217（217 aa） Chain IE 1–217（217 aa） Chain IF 1–217（217 aa） Chain IG 1–217（217 aa） Chain IH 1–217（217 aa） Chain II 1–217（217 aa） Chain IJ 1–217（217 aa） Chain IK 1–217（217 aa） Chain IL 1–217（217 aa） Chain IM 1–217（217 aa） Chain IN 1–217（217 aa） Chain IO 1–217（217 aa） Chain IP 1–217（217 aa） Chain IQ 1–217（217 aa） Chain IR 1–217（217 aa） Chain IS 1–217（217 aa） Chain IT 1–217（217 aa） Chain IU 1–217（217 aa） Chain IV 1–217（217 aa） Chain IW 1–217（217 aa） Chain IX 1–217（217 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 48 PDB declaration: 48-meric（48） Consistent with protein copy count	Chain OA； UniProt 1–219 Chain OB； UniProt 1–219 Chain OC； UniProt 1–219 Chain OD； UniProt 1–219 Chain OE； UniProt 1–219 Chain OF； UniProt 1–219 Chain OG； UniProt 1–219 Chain OH； UniProt 1–219 Chain OI； UniProt 1–219 Chain OJ； UniProt 1–219 Chain OK； UniProt 1–219 Chain OL； UniProt 1–219 Chain OM； UniProt 1–219 Chain ON； UniProt 1–219 Chain OO； UniProt 1–219 Chain OP； UniProt 1–219 Chain OQ； UniProt 1–219 Chain OR； UniProt 1–219 Chain OS； UniProt 1–219 Chain OT； UniProt 1–219 Chain OU； UniProt 1–219 Chain OV； UniProt 1–219 Chain OW； UniProt 1–219 Chain OX； UniProt 1–219	Not recorded	Gp77 × 24 （A0AAE8YXX1） ZN ZINC ION × 24	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	98.05 Å
Radius of gyration Rg (electron density) rg_electron	97.78 Å
Forward intensity I(0) i0	9368790000.00
Molecular weight molecular_weight	811360.0 kDa
Excluded volume excluded_volume	1008600 Å³
Envelope volume envelope_volume	1981200 Å³
Hydration-shell volume shell_volume	160400 Å³
Envelope diameter envelope_diameter	283.3 Å
Shell Rg shell_rg	105.10 Å
Envelope Rg envelope_rg	95.21 Å
Shape Rg shape_rg	97.71 Å
Total Rg total_rg	98.09 Å
Total atoms total_atoms	112779
Residues n_residues	7248
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	239.9 Å
Rg (real space) rg_real	94.36 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	9.0210e+09
I(0) uncertainty (real space) i0_real_error	1.5840e+08
Rg (reciprocal space) rg_reciprocal	97.17 Å
I(0) (reciprocal space) i0_reciprocal	9337000000.0000
Solution quality estimate total_estimate	0.9060
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	149.9 Å
Skewness Skewness skewness	-0.023
Kurtosis Kurtosis kurtosis	-0.924
Angular range angular_range	— – 0.0800 Å⁻¹
Current regularization parameter α current_alpha	0.3823
Highest regularization parameter α highest_alpha	221900000.0000
Real-space data points n_real_points	17
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.999; Stabil: 0.970; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Escherichia phage SECphi27
NCBI Class编号 ncbi_taxonomy_id	2496550
宿主生物 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

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 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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8. Citations (1)

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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测定方法 resolution_method	—
颗粒数 num_particles	28191

fit	/app/data/saxs_computation/y9/9y9c/9y9c.fit
pddf	/app/data/pr_computation/y9/9y9c/9y9c.pr.out
profile	/app/data/saxs_computation/y9/9y9c/9y9c.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)