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- PDB-6kz0: HRV14 3C in complex with single chain antibody GGVV -

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Basic information

Entry
Database: PDB / ID: 6kz0
TitleHRV14 3C in complex with single chain antibody GGVV
Components
  • GGVV H chain
  • GGVV L chain
  • Genome polyprotein
KeywordsVIRAL PROTEIN / protease / inhibitor / complex structure
Function / homology
Function and homology information


lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...lysis of host organelle involved in viral entry into host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman rhinovirus 14
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMeng, B. / Yang, B. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Inhibitory antibodies identify unique sites of therapeutic vulnerability in rhinovirus and other enteroviruses.
Authors: Meng, B. / Lan, K. / Xie, J. / Lerner, R.A. / Wilson, I.A. / Yang, B.
History
DepositionSep 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein
B: GGVV H chain
C: GGVV L chain
D: Genome polyprotein
E: GGVV H chain
F: GGVV L chain
G: Genome polyprotein
H: GGVV H chain
I: GGVV L chain
J: Genome polyprotein
K: GGVV H chain
L: GGVV L chain


Theoretical massNumber of molelcules
Total (without water)185,48912
Polymers185,48912
Non-polymers00
Water8,107450
1
A: Genome polyprotein
B: GGVV H chain
C: GGVV L chain


Theoretical massNumber of molelcules
Total (without water)46,3723
Polymers46,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-18 kcal/mol
Surface area16670 Å2
MethodPISA
2
D: Genome polyprotein
E: GGVV H chain
F: GGVV L chain


Theoretical massNumber of molelcules
Total (without water)46,3723
Polymers46,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-18 kcal/mol
Surface area16960 Å2
MethodPISA
3
G: Genome polyprotein
H: GGVV H chain
I: GGVV L chain


Theoretical massNumber of molelcules
Total (without water)46,3723
Polymers46,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-19 kcal/mol
Surface area17140 Å2
MethodPISA
4
J: Genome polyprotein
K: GGVV H chain
L: GGVV L chain


Theoretical massNumber of molelcules
Total (without water)46,3723
Polymers46,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-17 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.782, 133.256, 78.789
Angle α, β, γ (deg.)90.000, 93.545, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein
Genome polyprotein


Mass: 20166.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Production host: Escherichia coli (E. coli)
References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein
GGVV H chain


Mass: 14577.108 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody
GGVV L chain


Mass: 11629.018 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 0.1 M Tris-HCl, 25% MPEG5000, 0.2 M Li2SO4 / PH range: 8.5-8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. obs: 77385 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 26.64 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.093 / Rrim(I) all: 0.239 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5169 / CC1/2: 0.854 / Rpim(I) all: 0.376 / Rrim(I) all: 0.901 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IN2, 2GHW

2in2

2ghw


Resolution: 2.4→48.35 Å / SU ML: 0.2433 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.0658
RfactorNum. reflection% reflection
Rfree0.2234 3842 4.98 %
Rwork0.1853 --
obs0.1872 77222 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11966 0 0 450 12416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014512182
X-RAY DIFFRACTIONf_angle_d1.127916480
X-RAY DIFFRACTIONf_chiral_restr0.07511875
X-RAY DIFFRACTIONf_plane_restr0.00552107
X-RAY DIFFRACTIONf_dihedral_angle_d20.85024418
LS refinement shellResolution: 2.4→2.43 Å
RfactorNum. reflection% reflection
Rfree0.314 110 -
Rwork0.2484 1967 -
obs--72.29 %

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