SAXSdb — 9qgn

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

DUF4255 domain-containing protein

Photorhabdus luminescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Phage tail protein × 12 （A0A6L9JSR5） Phage tail sheath family protein × 6 （A0A6L9JN00）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6L9JUZ8_PHOLM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–300； UniProt 1–300 Author chain B； PDBConstruct 1–300； UniProt 1–300 Author chain C； PDBConstruct 1–300； UniProt 1–300 Author chain D； PDBConstruct 1–300； UniProt 1–300 Author chain E； PDBConstruct 1–300； UniProt 1–300 Author chain F； PDBConstruct 1–300； UniProt 1–300

Phage tail protein

Photorhabdus luminescens

UniProt A0A6L9JSR5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	DUF4255 domain-containing protein × 6 （A0A6L9JUZ8） Phage tail sheath family protein × 6 （A0A6L9JN00）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6L9JSR5_PHOLM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 1A； PDBConstruct 1–149； UniProt 1–149 Author chain 1B； PDBConstruct 1–149； UniProt 1–149 Author chain 1C； PDBConstruct 1–149； UniProt 1–149 Author chain 1D； PDBConstruct 1–149； UniProt 1–149 Author chain 1E； PDBConstruct 1–149； UniProt 1–149 Author chain 1F； PDBConstruct 1–149； UniProt 1–149 Author chain 1G； PDBConstruct 1–149； UniProt 1–149 Author chain 1H； PDBConstruct 1–149； UniProt 1–149 Author chain 1I； PDBConstruct 1–149； UniProt 1–149 Author chain 1J； PDBConstruct 1–149； UniProt 1–149 Author chain 1K； PDBConstruct 1–149； UniProt 1–149 Author chain 1L； PDBConstruct 1–149； UniProt 1–149

Phage tail sheath family protein

Photorhabdus luminescens

UniProt A0A6L9JN00

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	DUF4255 domain-containing protein × 6 （A0A6L9JUZ8） Phage tail protein × 12 （A0A6L9JSR5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6L9JN00_PHOLM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 2A； PDBConstruct 1–354； UniProt 1–354 Author chain 2B； PDBConstruct 1–354； UniProt 1–354 Author chain 2C； PDBConstruct 1–354； UniProt 1–354 Author chain 2D； PDBConstruct 1–354； UniProt 1–354 Author chain 2E； PDBConstruct 1–354； UniProt 1–354 Author chain 2F； PDBConstruct 1–354； UniProt 1–354

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	9qgn
Deposition date deposition_date	2025-03-14
Structure title title	Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state
Keywords keywords	Contractile injection system, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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.

9qgn__assembly_1__model_1

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

Download this curve (.dat)

9qgn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qgn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	57.05 Å
Rg (electron density)	56.28 Å
Total Rg	56.59 Å
Atom count	43476
Residues	5562
Excluded volume	775180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qgn__assembly_1__model_1`	24-meric （24）	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	DUF4255 domain-containing protein
Molecular weight formula_weight	33299.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	43476

MTIIIASDNAIIEINQALNTILSQYLNITGQNIDIRFDLPEINSIQSEPTVSVFLYEIHEDLQLRSAESRRYNPSTNTLLPGWVNINCNYLITYWDASKPSSDSSSPDSQPNNQAAQVMTRILNALINNRQLTGLPGAYTRIIPQQENLNSLGNFWQALGNRPRLSLLYSITVPMKLKNIEDNVIPVSKISASVDQKPNLDNSQINQALIDKLCVELGGTEDVRLALAKVNLTTKPDTENNQNQENESVIVEVSGITSVTYLPQIKDTLTKWKSSQEAIVKINGVSIVVSKENADKLIGI

Source Source

Source organism organism	Photorhabdus luminescens
NCBI taxonomy ID ncbi_taxonomy_id	29488
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Phage tail protein
Molecular weight formula_weight	16574.6 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1A,1B,1C,1D,1E,1F,1G,1H,1I,1J,1K,1L

MAITPEQIAVEYPIPTYRFVVSVGDEQIPFNNVSGLDVHYDVIEYKDGIGNYYKMPGQRQSINITLRKGVFPGDTKLFDWINSIQLNQVEKKDIAISLTNEAGTEILMTWNVANAFPTSFTSPSFDATSNEIAVQEIALTADRVTIQAA

Source Source

Source organism organism	Photorhabdus luminescens
NCBI taxonomy ID ncbi_taxonomy_id	29488
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Phage tail sheath family protein
Molecular weight formula_weight	39009.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2A,2B,2C,2D,2E,2F

MTTITTYPGVYIEEDASLSLSVSSSATAVPVFAVAGDNPLISGKPYIRISNWLEYLTLKNEQFDPANTLDISLRAYFINGGGYCYLVQTTDLEKQVPKLDDVTLLVAAGENITTAVSTLCKPGKGLFAIFDGPTTELKSDGTSNSDYDPNPFAAVYYPWLTADWTTTIDIPPSAAIAGVYCSVDSTRGVWKAPANVPIQGGLQPKYPVTDDLQAQYNQGKALNMIRTFPKSGTLVWGARTLEDNDNWRYIPVRRLFNSAERDIKNAMSFAVFEPNSQPTWERVRSAVNNYLYSLWQQGGLAGNKPDDAYFVQIGKDITMTDDDIKQGKMIIKIGMAAVRPAEFIILQFTQNTAQ

Source Source

Source organism organism	Photorhabdus luminescens
NCBI taxonomy ID ncbi_taxonomy_id	29488
Host organism host_organism	Escherichia coli

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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	2.46 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	57353

Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state

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

DUF4255 domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Phage tail protein

State in the Current Structure

Other States of the Same Protein in the Database

Phage tail sheath family 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

9qgn__assembly_1__model_1

9qgn__assembly_1__model_1 | I(q)

9qgn__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 polymer

Polymer Polymer

Source Source

7. Citations (1)

Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state

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

DUF4255 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

Phage tail 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

Phage tail sheath family 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

9qgn__assembly_1__model_1

9qgn__assembly_1__model_1 | I(q)

9qgn__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 polymer

Polymer Polymer

Source Source

7. Citations (1)