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- PDB-6kyz: HRV14 3C in complex with single chain antibody YDF -

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Basic information

Entry
Database: PDB / ID: 6kyz
TitleHRV14 3C in complex with single chain antibody YDF
Components
  • Genome polyprotein
  • YDF H chain
  • YDF L chain
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 / endocytosis involved in viral entry into host cell / : ...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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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: 1.845 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 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein
B: YDF H chain
C: YDF L chain
D: Genome polyprotein
E: YDF H chain
F: YDF L chain


Theoretical massNumber of molelcules
Total (without water)93,1826
Polymers93,1826
Non-polymers00
Water9,584532
1
A: Genome polyprotein
B: YDF H chain
C: YDF L chain


Theoretical massNumber of molelcules
Total (without water)46,5913
Polymers46,5913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-14 kcal/mol
Surface area17570 Å2
MethodPISA
2
D: Genome polyprotein
E: YDF H chain
F: YDF L chain


Theoretical massNumber of molelcules
Total (without water)46,5913
Polymers46,5913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-14 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.335, 120.846, 71.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Genome polyprotein


Mass: 20166.008 Da / Num. of mol.: 2
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: Antibody YDF H chain


Mass: 15125.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody YDF L chain


Mass: 11299.447 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M citrate 40% PEG600 / PH range: 5.3-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 1.845→50 Å / Num. obs: 80114 / % possible obs: 99.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.051 / Rrim(I) all: 0.182 / Net I/σ(I): 20
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2300 / CC1/2: 0.852 / Rpim(I) all: 0.182 / Rrim(I) all: 0.528 / % possible all: 95.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IN2, 2GHW

2in2

2ghw


Resolution: 1.845→49.048 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.91
RfactorNum. reflection% reflection
Rfree0.2081 3973 4.96 %
Rwork0.1745 --
obs0.1761 80053 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.02 Å2 / Biso mean: 23.4076 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 1.845→49.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6281 0 0 532 6813
Biso mean---32.46 -
Num. residues----824
LS refinement shellResolution: 1.8452→1.8677 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2243 129 -
Rwork0.1949 2300 -
obs--86 %

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