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- PDB-9xqs: Structure of the inner peripheral region in the phage phiKZ basep... -

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Basic information

Entry
Database: PDB / ID: 9xqs
TitleStructure of the inner peripheral region in the phage phiKZ baseplate complex
Components
  • PHIKZ029
  • PHIKZ049
  • PHIKZ062
  • PHIKZ087
  • PHIKZ088
  • PHIKZ128
  • PHIKZ161
  • PHIKZ182
KeywordsVIRAL PROTEIN / baseplate / inner peripheral
Function / homology
Function and homology information


SH3 fold domain associated with phage DNA polymerases / : / : / SH3 fold domain associated with phage DNA polymerases / Family of unknown function (DUF7194) / Putative phage tail tube protein / : / Bacteriophage phiKZ, gp29PR
Similarity search - Domain/homology
PHIKZ182 / PHIKZ161 / PHIKZ128 / PHIKZ088 / PHIKZ087 / PHIKZ062 / PHIKZ049 / PHIKZ029
Similarity search - Component
Biological speciesPseudomonas phage phiKZ (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsXiao, H. / Peng, Z. / Zhou, J. / Liu, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: To Be Published
Title: Structural atlas of the intact jumbo phage phiKZ
Authors: Xiao, H. / Peng, Z. / Zhou, J. / Liu, H.
History
DepositionNov 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHIKZ087
B: PHIKZ087
C: PHIKZ128
D: PHIKZ128
E: PHIKZ161
F: PHIKZ161
G: PHIKZ161
H: PHIKZ161
I: PHIKZ088
J: PHIKZ088
K: PHIKZ182
L: PHIKZ182
M: PHIKZ049
N: PHIKZ049
O: PHIKZ049
P: PHIKZ049
Q: PHIKZ049
R: PHIKZ049
S: PHIKZ049
T: PHIKZ049
U: PHIKZ087
V: PHIKZ087
W: PHIKZ029
X: PHIKZ029
Y: PHIKZ029
Z: PHIKZ029
a: PHIKZ062
b: PHIKZ062


Theoretical massNumber of molelcules
Total (without water)1,392,21628
Polymers1,392,21628
Non-polymers00
Water00
1
A: PHIKZ087
B: PHIKZ087
C: PHIKZ128
D: PHIKZ128
E: PHIKZ161
F: PHIKZ161
G: PHIKZ161
H: PHIKZ161
I: PHIKZ088
J: PHIKZ088
K: PHIKZ182
L: PHIKZ182
M: PHIKZ049
N: PHIKZ049
O: PHIKZ049
P: PHIKZ049
Q: PHIKZ049
R: PHIKZ049
S: PHIKZ049
T: PHIKZ049
U: PHIKZ087
V: PHIKZ087
W: PHIKZ029
X: PHIKZ029
Y: PHIKZ029
Z: PHIKZ029
a: PHIKZ062
b: PHIKZ062

A: PHIKZ087
B: PHIKZ087
C: PHIKZ128
D: PHIKZ128
E: PHIKZ161
F: PHIKZ161
G: PHIKZ161
H: PHIKZ161
I: PHIKZ088
J: PHIKZ088
K: PHIKZ182
L: PHIKZ182
M: PHIKZ049
N: PHIKZ049
O: PHIKZ049
P: PHIKZ049
Q: PHIKZ049
R: PHIKZ049
S: PHIKZ049
T: PHIKZ049
U: PHIKZ087
V: PHIKZ087
W: PHIKZ029
X: PHIKZ029
Y: PHIKZ029
Z: PHIKZ029
a: PHIKZ062
b: PHIKZ062

A: PHIKZ087
B: PHIKZ087
C: PHIKZ128
D: PHIKZ128
E: PHIKZ161
F: PHIKZ161
G: PHIKZ161
H: PHIKZ161
I: PHIKZ088
J: PHIKZ088
K: PHIKZ182
L: PHIKZ182
M: PHIKZ049
N: PHIKZ049
O: PHIKZ049
P: PHIKZ049
Q: PHIKZ049
R: PHIKZ049
S: PHIKZ049
T: PHIKZ049
U: PHIKZ087
V: PHIKZ087
W: PHIKZ029
X: PHIKZ029
Y: PHIKZ029
Z: PHIKZ029
a: PHIKZ062
b: PHIKZ062


Theoretical massNumber of molelcules
Total (without water)4,176,64784
Polymers4,176,64784
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

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Protein , 8 types, 28 molecules ABUVCDEFGHIJKLMNOPQRSTWXYZab

#1: Protein
PHIKZ087


Mass: 110486.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SD75
#2: Protein PHIKZ128


Mass: 84297.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SD34
#3: Protein
PHIKZ161


Mass: 22584.465 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SD01
#4: Protein PHIKZ088


Mass: 40503.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SD74
#5: Protein PHIKZ182


Mass: 73539.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SCY0
#6: Protein
PHIKZ049


Mass: 15212.229 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SDB3
#7: Protein
PHIKZ029


Mass: 77712.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SDD3
#8: Protein PHIKZ062


Mass: 15352.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SDA0

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pseudomonas phage phiKZ / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22539 / Symmetry type: POINT
RefinementHighest resolution: 3.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00393744
ELECTRON MICROSCOPYf_angle_d0.569127410
ELECTRON MICROSCOPYf_dihedral_angle_d5.32212902
ELECTRON MICROSCOPYf_chiral_restr0.04314364
ELECTRON MICROSCOPYf_plane_restr0.00416574

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