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- PDB-6u8d: Crystal structure of hepatitis C virus IRES junction IIIabc in co... -

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Basic information

Entry
Database: PDB / ID: 6u8d
TitleCrystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV2
Components
  • Heavy chain of Fab HCV2
  • JIIIabc RNA (68-MER)
  • Light chain of Fab HCV2
KeywordsRNA/Immune System / Internal ribosome entry site (IRES) / hepatitis C virus / Junction IIIabc / Antibody-assisted RNA crystallography / Viral translation / Viral RNA domains / RNA / RNA-Immune System complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
Hepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.807 Å
AuthorsKoirala, D. / Lewicka, A. / Koldobskaya, Y. / Huang, H. / Piccirilli, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI081987 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM102489 United States
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation.
Authors: Koirala, D. / Lewicka, A. / Koldobskaya, Y. / Huang, H. / Piccirilli, J.A.
History
DepositionSep 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: JIIIabc RNA (68-MER)
H: Heavy chain of Fab HCV2
L: Light chain of Fab HCV2


Theoretical massNumber of molelcules
Total (without water)70,4453
Polymers70,4453
Non-polymers00
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-32 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.705, 161.223, 96.978
Angle α, β, γ (deg.)90.000, 102.660, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: RNA chain JIIIabc RNA (68-MER)


Mass: 22014.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: JIIIabc of hepatitis C virus IRES / Source: (synth.) Hepacivirus C
#2: Antibody Heavy chain of Fab HCV2


Mass: 25019.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Heavy chain of Fab HCV2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Light chain of Fab HCV2


Mass: 23410.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Light chain of Fab HCV2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M bis-tris pH 5.5, 45% 2-methyl-2,4-pentanediaol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.807→61.362 Å / Num. obs: 67168 / % possible obs: 98.73 % / Redundancy: 3.9 % / Biso Wilson estimate: 40.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04042 / Rpim(I) all: 0.0232 / Rrim(I) all: 0.04674 / Net I/σ(I): 15.66
Reflection shellResolution: 1.807→1.872 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.134 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 6420 / CC1/2: 0.481 / Rpim(I) all: 0.6692 / % possible all: 94.58

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab HAVx, 6MWN

6mwn


Resolution: 1.807→61.362 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.06
RfactorNum. reflection% reflection
Rfree0.2088 2005 2.99 %
Rwork0.1735 --
obs0.1746 67011 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.41 Å2 / Biso mean: 55.9495 Å2 / Biso min: 26.68 Å2
Refinement stepCycle: final / Resolution: 1.807→61.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 1460 0 386 5188
Biso mean---56.71 -
Num. residues----508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8072-1.85240.3482143434293
1.8524-1.90250.3584130467499
1.9025-1.95850.3346149462699
1.9585-2.02170.2958144463999
2.0217-2.09390.317141460098
2.0939-2.17780.28741464703100
2.1778-2.27690.26451454672100
2.2769-2.39690.22961454665100
2.3969-2.54710.2227141469799
2.5471-2.74380.2383146466899
2.7438-3.01990.277142460098
3.0199-3.45680.25921404689100
3.4568-4.35510.15931430.13614704100
4.35510.14121500.1257472799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61270.0030.62210.72950.33051.7807-0.1160.24620.0156-0.1744-0.0179-0.028-0.28190.46990.07660.336-0.049-0.00970.52060.01010.399540.04148.27923.626
21.12570.81070.52151.6133-0.10810.81390.1279-0.0563-0.0784-0.08820.09650.24240.4323-0.077-0.13720.4737-0.0049-0.10130.32920.0010.3722.28913.02314.131
30.46460.32870.47111.8064-0.03320.79370.2032-0.1558-0.17880.2773-0.00240.0790.5251-0.1335-0.14820.5233-0.0665-0.05390.36710.03310.37330.7948.86130.929
40.24730.13560.20690.2841-0.09080.47550.0273-0.00610.0103-0.0362-0.00770.00290.10780.0825-0.02130.35920.0253-0.00760.4136-0.02240.3919.36230.51723.837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 143:248 )A143 - 248
2X-RAY DIFFRACTION2( CHAIN H AND RESID 4:228 )H4 - 228
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:215 )L1 - 215
4X-RAY DIFFRACTION4( CHAIN A AND RESID 301:459 ) OR ( CHAIN H AND RESID 301:424 ) OR ( CHAIN L AND RESID 301:403 )A301 - 459
5X-RAY DIFFRACTION4( CHAIN A AND RESID 301:459 ) OR ( CHAIN H AND RESID 301:424 ) OR ( CHAIN L AND RESID 301:403 )H301 - 424
6X-RAY DIFFRACTION4( CHAIN A AND RESID 301:459 ) OR ( CHAIN H AND RESID 301:424 ) OR ( CHAIN L AND RESID 301:403 )L301 - 403

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