SAXSdb — 8q7d

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

Putative neck protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Portal protein × 12 （A0A0U1WIV9） DNA forward strand (120-MER) × 1 DNA reverse strand (120-MER) × 1 ZINC ION × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1YTN6_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain d； PDBConstruct 1–302； UniProt 1–302

Portal protein

OrganismNot specified

UniProt A0A0U1WIV9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 24 DNA 2	Putative neck protein × 12 （A1YTN6） DNA forward strand (120-MER) × 1 DNA reverse strand (120-MER) × 1 ZINC ION × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0U1WIV9_9CAUD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain p； PDBConstruct 1–563； UniProt 1–563

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	8q7d
Deposition date deposition_date	2023-08-16
Structure title title	Neck of phage 812 after tail contraction (C12)
Keywords keywords	phage, neck, portal, connector, VIRUS; VIRUS
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.

8q7d__assembly_1__model_1

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

Download this curve (.dat)

8q7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8q7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	68.37 Å
Rg (electron density)	66.69 Å
Total Rg	67.24 Å
Atom count	72732
Residues	8640
Excluded volume	1277500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8q7d__assembly_1__model_1`	26-meric （26）	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	Putative neck protein
Molecular weight formula_weight	34191.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d
Atom count atom_count	10571

MVNSMFGGDLDPYEKSLNYEYPYHPSGNPKHIDVSEIDNLTLADYGWSPDAVKAYMFGIVVQNPDTGQPMGDEFYNHILERAVGKAERALDISILPDTQHEMRDYHETEFNSYMFVHAYRKPILQVENLQLQFNGRPIYKYPANWWKVEHLAGHVQLFPTALMQTGQSMSYDAVFNGYPQLAGVYPPSGATFAPQMIRLEYVSGMLPRKKAGRNKPWEMPPELEQLVIKYALKEIYQVWGNLIIGAGIANKTLEVDGITETIGTTQSAMYGGASAQILQINEDIKELLDGLRAYFGYNMIGL

Entity 2 Entity 2 polymer

Description description	Portal protein
Molecular weight formula_weight	64155.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

MADLFKQFRLGKDYGNNSTIAQVPIDEGLQANIKKIEQDNKEYQDLTKSLYGQQQAYAEPFIEMMDTNPEFRDKRSYMKNEHNLHDVLKKFGNNPILNAIILTRSNQVAMYCQPARYSEKGLGFEVRLRDLDAEPGRKEKEEMKRIEDFIVNTGKDKDVDRDSFQTFCKKIVRDTYIYDQVNFEKVFNKNNKTKLEKFIAVDPSTIFYATDKKGKIIKGGKRFVQVVDKRVVASFTSRELAMGIRNPRTELSSSGYGLSEVEIAMKEFIAYNNTESFNDRFFSHGGTTRGILQIRSDQQQSQHALENFKREWKSSLSGINGSWQIPVVMADDIKFVNMTPTANDMQFEKWLNYLINIISALYGIDPAEIGFPNRGGATGSKGGSTLNEADPGKKQQQSQNKGLQPLLRFIEDLVNRHIISEYGDKYTFQFVGGDTKSATDKLNILKLETQIFKTVNEAREEQGKKPIEGGDIILDASFLQGTAQLQQDKQYNDGKQKERLQMMMSLLEGDNDDSEEGQSTDSSNDDKEIGTDAQIKGDDNVYRTQTSNKGQGRKGEKSSDFKH

Entity 3 Entity 3 polymer

Description description	DNA forward strand (120-MER)
Molecular weight formula_weight	36242.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

TACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATCTACACTTATC

Entity 4 Entity 4 polymer

Description description	DNA reverse strand (120-MER)
Molecular weight formula_weight	37791.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Z

GATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTAGATAAGTGTA

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	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	3.07 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	17304

Neck of phage 812 after tail contraction (C12)

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

Putative neck protein

State in the Current Structure

Other States of the Same Protein in the Database

Portal 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

8q7d__assembly_1__model_1

8q7d__assembly_1__model_1 | I(q)

8q7d__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Neck of phage 812 after tail contraction (C12)

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

Putative neck 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

Portal 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

8q7d__assembly_1__model_1

8q7d__assembly_1__model_1 | I(q)

8q7d__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)