SAXSdb — 9yft

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

Gp53

OrganismNot specified

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 × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain FA； UniProt 1–885	Not recorded	Non-contractile tail sheath × 1 （A0MZE7） Gp54 × 12 （Q859Q3）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.61 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	Q859Q2_BPN4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain FA； PDBConstruct 1–885； UniProt 1–885

Non-contractile tail sheath

OrganismNot specified

UniProt A0MZE7

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 × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain LA； UniProt 1–1382	Not recorded	Gp53 × 1 （Q859Q2） Gp54 × 12 （Q859Q3）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.61 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 9YFT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9LC0 tail complex of mature phage N4 Deposited 2025-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain I 1–1382（1382 aa） Chain N 1–1382（1382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9LC0 tail complex of mature phage N4 Deposited 2025-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain I 1–1382（1382 aa） Chain N 1–1382（1382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9LC0 tail complex of mature phage N4 Deposited 2025-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain I 1–1382（1382 aa） Chain N 1–1382（1382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9YF4 N4 Full Virion C6 Tail Deposited 2025-09-25	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 96 PDB declaration: 96-meric	Chain LA 1–1382（1382 aa） Chain LB 1–1382（1382 aa） Chain LC 1–1382（1382 aa） Chain LD 1–1382（1382 aa） Chain LE 1–1382（1382 aa） Chain LF 1–1382（1382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.28 Å
9YF5 N4 Empty Particle C6 Tail Deposited 2025-09-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain LA 1–1382（1382 aa） Chain LB 1–1382（1382 aa） Chain LC 1–1382（1382 aa） Chain LD 1–1382（1382 aa） Chain LE 1–1382（1382 aa） Chain LF 1–1382（1382 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCTSP_BPN4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain LA； PDBConstruct 1–1382； UniProt 1–1382

Gp54

OrganismNot specified

UniProt Q859Q3

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 × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain TA； UniProt 1–299 Chain TB； UniProt 1–299 Chain TC； UniProt 1–299 Chain TD； UniProt 1–299 Chain TE； UniProt 1–299 Chain TF； UniProt 1–299 Chain TG； UniProt 1–299 Chain TH； UniProt 1–299 Chain TI； UniProt 1–299 Chain TJ； UniProt 1–299 Chain TK； UniProt 1–299 Chain TL； UniProt 1–299	Not recorded	Gp53 × 1 （Q859Q2） Non-contractile tail sheath × 1 （A0MZE7）	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.61 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 9YFT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9LC0 tail complex of mature phage N4 Deposited 2025-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain K 1–299（299 aa） Chain P 1–299（299 aa） Chain T 1–299（299 aa） Chain U 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9LC0 tail complex of mature phage N4 Deposited 2025-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain K 1–299（299 aa） Chain P 1–299（299 aa） Chain T 1–299（299 aa） Chain U 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9LC0 tail complex of mature phage N4 Deposited 2025-01-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain K 1–299（299 aa） Chain P 1–299（299 aa） Chain T 1–299（299 aa） Chain U 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9YF4 N4 Full Virion C6 Tail Deposited 2025-09-25	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 96 PDB declaration: 96-meric	Chain TA 1–299（299 aa） Chain TB 1–299（299 aa） Chain TC 1–299（299 aa） Chain TD 1–299（299 aa） Chain TE 1–299（299 aa） Chain TF 1–299（299 aa） Chain TG 1–299（299 aa） Chain TH 1–299（299 aa） Chain TI 1–299（299 aa） Chain TJ 1–299（299 aa） Chain TK 1–299（299 aa） Chain TL 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.28 Å
9YF5 N4 Empty Particle C6 Tail Deposited 2025-09-25	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain TA 1–299（299 aa） Chain TB 1–299（299 aa） Chain TC 1–299（299 aa） Chain TD 1–299（299 aa） Chain TE 1–299（299 aa） Chain TF 1–299（299 aa） Chain TG 1–299（299 aa） Chain TH 1–299（299 aa） Chain TI 1–299（299 aa） Chain TJ 1–299（299 aa） Chain TK 1–299（299 aa） Chain TL 1–299（299 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q859Q3_BPN4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain TA； PDBConstruct 1–299； UniProt 1–299 Author chain TB； PDBConstruct 1–299； UniProt 1–299 Author chain TC； PDBConstruct 1–299； UniProt 1–299 Author chain TD； PDBConstruct 1–299； UniProt 1–299 Author chain TE； PDBConstruct 1–299； UniProt 1–299 Author chain TF； PDBConstruct 1–299； UniProt 1–299 Author chain TG； PDBConstruct 1–299； UniProt 1–299 Author chain TH； PDBConstruct 1–299； UniProt 1–299 Author chain TI； PDBConstruct 1–299； UniProt 1–299 Author chain TJ； PDBConstruct 1–299； UniProt 1–299 Author chain TK； PDBConstruct 1–299； UniProt 1–299 Author chain TL； PDBConstruct 1–299； UniProt 1–299

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	9yft
Deposition date deposition_date	2025-09-26
Structure title title	N4 Bacteriophage Asymmetric Tail Gating Complex
Keywords keywords	bacteriophage, VIRAL PROTEIN; VIRAL 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	49.70 Å
Radius of gyration Rg (electron density) rg_electron	51.32 Å
Forward intensity I(0) i0	599545000.00
Molecular weight molecular_weight	200940.0 kDa
Excluded volume excluded_volume	251160 Å³
Envelope volume envelope_volume	362150 Å³
Hydration-shell volume shell_volume	66613 Å³
Envelope diameter envelope_diameter	230.0 Å
Shell Rg shell_rg	47.71 Å
Envelope Rg envelope_rg	54.49 Å
Shape Rg shape_rg	51.31 Å
Total Rg total_rg	51.21 Å
Total atoms total_atoms	14173
Residues n_residues	1832
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	133.1 Å
Rg (real space) rg_real	44.28 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	5.6800e+08
I(0) uncertainty (real space) i0_real_error	8.2500e+06
Rg (reciprocal space) rg_reciprocal	49.71 Å
I(0) (reciprocal space) i0_reciprocal	597800000.0000
Solution quality estimate total_estimate	0.7231
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.9 Å
Skewness Skewness skewness	0.482
Kurtosis Kurtosis kurtosis	-0.196
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.1040
Highest regularization parameter α highest_alpha	60650000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.010; Oscil: 0.898; Stabil: 0.989; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.784

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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	Gp53
Molecular weight formula_weight	97954.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	FA
Atom count atom_count	14173

MGLFSSKTKIYVASSVYNLAGDIHKRPNYLKTTVIGNIVSKSDFSMGDTITDSYLNGPGIRLRRFPGWAATNYDPSIGIAYGNLSILSQVDPEVVKWQVPQKAGYEVQVQSSRIGFGDFEEWADKFLYENYPDRITEEFEIDIMDDDRIVLTATDGSELSFYPKNYSQDAMYLYVNYYYIQPTSVADPVVHPAVSVSSADDLPSTSEWTQVSQNHTPKSATLKTVTHIKSVFSDGRPDEESTNTEEEQVSWTNFSDVYEKEFREPSEVGLIIIRKTIMTQVQTGTVSTGSTTNTEVIDLGGGVTETRTTTVTTDTLGHTWSYQNTDVVTTLSAGGMPQLFIYKQNSGNAVLDALFINKTTNNRFYSFIPIRSDKNWISGSTYTLCKKAFKKATGGKISDIMDDLKKNKDIGDIQYIYAVFGCSLNSPENTAKEYIYRFFQLVNQSMPADPNYPTMDALVEGFAQANRDFDAYQEWWESRSGNRDIPIGKPPKRPVYPTIPSKSINIRSNGGYRYNMTISWNFIEESVGSGKAFSGAKKGQLKFAYEGTVVLMQKAVMYSEKGNDKVGFTIYRLDKITMYWQDGDNSWRKISVYGLNHNNNVYKNKSVSISGVDALNDDEESGFIIPLHNNIYRSMSLVNGTQLSTACCYLVLNSYKKVKKKWYQSGIFKVVVVVVAVVVSVFFTPAAGAGVMGTAASIGAALGFAGLAAIIVGAVANAIAAMILMSIIQTVSVSLLGDKIGIIVATIASMVAMNVGTALSTGSSMSTMLGEMMKADNIIKLTSSVGNGISDYINASAMETVKKTEKLMAEYRDQMKTIQEKYEEMFGTEGMGYIDPMNLTNVGQQFEPLDSFLSRTLMTGHDIADMSNNMITNFTDITLQLDLDT

Entity 2 Entity 2 polymer

Description description	Non-contractile tail sheath
Molecular weight formula_weight	154255.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	LA

MSIEDYLKGKNCLASPNYDPDDQHSSWREDLPQFKKDREHLTLVNTRRNRTYNTKLNRFDPEYWVVDYNALMVATIIPYGSKSFKVPCQWRTNKDFLGVRWMTEDTFDHHLYRYETDPNYLGLILAFRHNPDEPDKFTVTIQTPEKAYTYRLAPYGFNNKTRRWECLDTKYGTKRTYQADIFVATDEDIPESEMTEVYGTKDYIFILDFADLRTGVAFNGVTINPRNITMISFDCTEAHHGLGKDAYIAAMYNNDDGATFQMEIGGIHTNAALAAGDKLQCIWRYLDVNGNAQAAENEFEVVSYEGFGTSNFSVKCKGMLPGKFIGCDAFYGKYLQTDGPIKQVDSVKWFTNLTVSGSGRKQLGQRKYPQVVMGMGMTSGFDDGYNLTPERQVKMAYGLGYRDWWTTYIGMSHYWKGLTAFQDKETGELITEQTVLDYPILFAGESQVAIHFMSGAYPDRGYDVFQKYMTETWGINYAGVHPINGTTGSTAVDRACAVNPNSEVFDPTQSSGAGGLWWWDLEADKPGPALLHCVGQVGKLKPKAIIWGQGDQDATALAYPGDRNPAPSLTRTKQATKKVFEYLRSLYGQIPIFIQELSYAWGITNTDAPNVPIRTGLPSFLAARRNTWGDIEFRWKSYGLDPALAQYRIEIYNPSNLNQILHSFVVSGTQEANGYVYADFTVEDWIPVMMEAVGSPNPWEFMKWRVVCLYQEREIPSAPWSDNIPLDNAGLVKKTILVGINQFGGGHFTDMSDPTATTANGAIGRKDKVSASTLRLTFAEKAGLRPIQVMPVNVAADSAGMTVGTHKWWNTSSNSPGDALLAINDMVKGLGVKPDYFIEANPWETMYMKDVNSSTWPALMTAFESSNKAMLAWMRTNWGNPNLEIWFQGATTVWFGVAPPNDLNSEATVTVRDKQIQMATANIGFKLGSFVPGSNLYTAYRNVESSWIYYTVEAFHATAIELGEALALNINRATNPPDWSYLRPPANLQGRKLATRDIKMTWDNRAGITHWKYANRHVTTGAEISSGILTSPEYVFTLNDQQNAYNGDTLNMSFSVSEYAADSGAVGASSSFVGVVQNGSYMQTPTQLKAAKQLNGDIIFTWVGRPSWQHFWVVNTSVNDSKTVIFSKEWSSESLTWTVAEQNEFYGLEEGGATHVIFMVSEYDPSNGLVSIGAQVTGQAEQPSNPMNPVAGLYAVFTGDPGNSNIKIMWDKPSVGGRDVRIRNMHVTSSATISDQFVSDNNLVFTREEQVAAYGFTASSVSVRAQEHDIESGALGLTTEYVAVPETAGTVGQGFAKKDSVGNCTMSWEVGDAVQWQVEILNAENSTVVKTEIVVAPTITWMAEEITAEYGYLTDHMVWRVRPYRADGASNVAKQFDMTATL

Entity 3 Entity 3 polymer

Description description	Gp54
Molecular weight formula_weight	32438.4 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	TA,TB,TC,TD,TE,TF,TG,TH,TI,TJ,TK,TL

MSCGAELEANALLTALVAGEDFTLPDIDMSGSEYDIPGGINSPIYAEIEKITTEQLTTREVGGSGVFDALMQSASNHLLAEFKNNRITGGDYVKAYIATMEACMANAVQFLTTKDQAYWNAVTAQVAAITARANLGIIKANFVTAKIQALATKAEYALTKLKLSNESVTYCTAQYNLSSMLPQQLLMLKNQTTQVAEQTKLTTEQINMTKEQKEAQRAQTSDTRTDGTRVAGSVGKQKELYDQQITSYKRDAEVKAAKLFTDAWVTQKTIDEGLSPPNGFTNSSLDSILTALKNNNALG

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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	3.61 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	18434

fit	/app/data/saxs_computation/yf/9yft/9yft.fit
pddf	/app/data/pr_computation/yf/9yft/9yft.pr.out
profile	/app/data/saxs_computation/yf/9yft/9yft.dat

N4 Bacteriophage Asymmetric Tail Gating Complex

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

Gp53

State in the Current Structure

Other States of the Same Protein in the Database

Non-contractile tail sheath

State in the Current Structure

Other States of the Same Protein in the Database

Gp54

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)