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- PDB-6cgr: CryoEM structure of herpes simplex virus 1 capsid with associated... -

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Basic information

Entry
Database: PDB / ID: 6cgr
TitleCryoEM structure of herpes simplex virus 1 capsid with associated tegument protein complexes.
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • Small capsomere-interacting protein
KeywordsVIRUS / human herpesvirus 1 / Herpes simplex virus type 1 / capsid-associated tegument complex
Function / homology
Function and homology information


deNEDDylase activity / T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid ...deNEDDylase activity / T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral process / chromosome organization / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Herpesvirus UL35 / Herpesvirus UL35 family / Large tegument protein deneddylase / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus capsid shell protein 1 / Herpesvirus capsid shell protein VP19C / Herpesvirus capsid protein 2 / Herpesvirus VP23 like capsid protein / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Capsid triplex subunit 1 / UL17 / Capsid triplex subunit 2 / Major capsid protein / DNA packaging tegument protein UL25 / Large tegument protein / Small capsomere-interacting protein
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDai, X.H. / Zhou, Z.H.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Science / Year: 2018
Title: Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes.
Authors: Xinghong Dai / Z Hong Zhou /
Abstract: Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. ...Herpes simplex viruses (HSVs) rely on capsid-associated tegument complex (CATC) for long-range axonal transport of their genome-containing capsids between sites of infection and neuronal cell bodies. Here we report cryo-electron microscopy structures of the HSV-1 capsid with CATC up to 3.5-angstrom resolution and atomic models of multiple conformers of capsid proteins VP5, VP19c, VP23, and VP26 and tegument proteins pUL17, pUL25, and pUL36. Crowning every capsid vertex are five copies of heteropentameric CATC, each containing a pUL17 monomer supporting the coiled-coil helix bundle of a pUL25 dimer and a pUL36 dimer, thus positioning their flexible domains for potential involvement in nuclear capsid egress and axonal capsid transport. Notwithstanding newly discovered fold conservation between triplex proteins and bacteriophage λ protein gpD and the previously recognized bacteriophage HK97 gp5-like fold in VP5, HSV-1 capsid proteins exhibit extraordinary diversity in forms of domain insertion and conformational polymorphism, not only for interactions with tegument proteins but also for encapsulation of large genomes.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Superimposition on EM map
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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
k: Capsid vertex component 1
l: Capsid vertex component 2
m: Capsid vertex component 2
n: Large tegument protein deneddylase
o: Large tegument protein deneddylase


Theoretical massNumber of molelcules
Total (without water)4,031,74451
Polymers4,031,74451
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
k: Capsid vertex component 1
l: Capsid vertex component 2
m: Capsid vertex component 2
n: Large tegument protein deneddylase
o: Large tegument protein deneddylase
x 60


Theoretical massNumber of molelcules
Total (without water)241,904,6383060
Polymers241,904,6383060
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
k: Capsid vertex component 1
l: Capsid vertex component 2
m: Capsid vertex component 2
n: Large tegument protein deneddylase
o: Large tegument protein deneddylase
x 5


  • icosahedral pentamer
  • 20.2 MDa, 255 polymers
Theoretical massNumber of molelcules
Total (without water)20,158,720255
Polymers20,158,720255
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Small capsomere-interacting protein
H: Small capsomere-interacting protein
I: Small capsomere-interacting protein
J: Small capsomere-interacting protein
K: Small capsomere-interacting protein
L: Small capsomere-interacting protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Small capsomere-interacting protein
Q: Small capsomere-interacting protein
R: Small capsomere-interacting protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Small capsomere-interacting protein
Z: Small capsomere-interacting protein
0: Small capsomere-interacting protein
1: Small capsomere-interacting protein
2: Small capsomere-interacting protein
3: Small capsomere-interacting protein
4: Major capsid protein
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
8: Triplex capsid protein 1
9: Triplex capsid protein 2
a: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
e: Triplex capsid protein 1
f: Triplex capsid protein 2
g: Triplex capsid protein 2
h: Triplex capsid protein 1
i: Triplex capsid protein 2
j: Triplex capsid protein 2
k: Capsid vertex component 1
l: Capsid vertex component 2
m: Capsid vertex component 2
n: Large tegument protein deneddylase
o: Large tegument protein deneddylase
x 6


  • icosahedral 23 hexamer
  • 24.2 MDa, 306 polymers
Theoretical massNumber of molelcules
Total (without water)24,190,464306
Polymers24,190,464306
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 3 types, 33 molecules ABCDEFMNOSTUVWX4GHIJKLPQRYZ012...

#1: Protein
Major capsid protein / MCP


Mass: 149229.047 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: G8HBD2
#2: Protein
Small capsomere-interacting protein


Mass: 12108.655 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: Q25BW6
#7: Protein Large tegument protein deneddylase


Mass: 333809.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: G8HBF0, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Triplex capsid protein ... , 2 types, 15 molecules 58beh679acdfgij

#3: Protein
Triplex capsid protein 1


Mass: 50328.281 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: F8REX2
#4: Protein
Triplex capsid protein 2


Mass: 34301.617 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: G8H8D9

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Capsid vertex component ... , 2 types, 3 molecules klm

#5: Protein Capsid vertex component 1


Mass: 74699.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: F8RFA1
#6: Protein Capsid vertex component 2


Mass: 62736.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: G8HBD8

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Details

Has protein modificationY

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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: Human herpesvirus 1 strain KOS / Type: VIRUS / Details: Cultured in Vero cells. / Entity ID: all / Source: NATURAL
Molecular weightValue: 200 MDa / Experimental value: NO
Source (natural)Organism: Human herpesvirus 1 strain KOS
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 1300 nm / Triangulation number (T number): 16
Buffer solutionpH: 7.4
Buffer componentName: phosphate buffered saline / Formula: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 298 K
Details: The sample was manually blotted and frozen with a homemade plunger.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 14000 X / Calibrated magnification: 24271 X / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 79 K
Image recordingAverage exposure time: 13 sec. / Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 7356
Image scansSampling size: 2.5 µm / Width: 7676 / Height: 7420 / Movie frames/image: 26 / Used frames/image: 1-26

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Processing

SoftwareName: PHENIX / Version: dev_2875: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND3CTF correction
9IMIRSinitial Euler assignment
10IMIRSfinal Euler assignment
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 45530
Details: Particles were boxed with ETHAN, and then manually examined.
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28042 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007225010
ELECTRON MICROSCOPYf_angle_d0.954307131
ELECTRON MICROSCOPYf_dihedral_angle_d4.089134710
ELECTRON MICROSCOPYf_chiral_restr0.05334661
ELECTRON MICROSCOPYf_plane_restr0.00740948

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