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- PDB-6u8k: Crystal structure of hepatitis C virus IRES junction IIIabc in co... -

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Basic information

Entry
Database: PDB / ID: 6u8k
TitleCrystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV3
Components
  • Heavy chain of Fab HCV3
  • JIIIabc RNA (68-MER)
  • Light chain of Fab HCV3
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: 2.75 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 5, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JIIIabc RNA (68-MER)
B: JIIIabc RNA (68-MER)
C: JIIIabc RNA (68-MER)
D: Heavy chain of Fab HCV3
E: Light chain of Fab HCV3
F: Heavy chain of Fab HCV3
G: Light chain of Fab HCV3
H: Heavy chain of Fab HCV3
L: Light chain of Fab HCV3


Theoretical massNumber of molelcules
Total (without water)210,3719
Polymers210,3719
Non-polymers00
Water2,882160
1
A: JIIIabc RNA (68-MER)
H: Heavy chain of Fab HCV3
L: Light chain of Fab HCV3


Theoretical massNumber of molelcules
Total (without water)70,1243
Polymers70,1243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-43 kcal/mol
Surface area29750 Å2
MethodPISA
2
B: JIIIabc RNA (68-MER)
D: Heavy chain of Fab HCV3
E: Light chain of Fab HCV3


Theoretical massNumber of molelcules
Total (without water)70,1243
Polymers70,1243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-41 kcal/mol
Surface area29890 Å2
MethodPISA
3
C: JIIIabc RNA (68-MER)
F: Heavy chain of Fab HCV3
G: Light chain of Fab HCV3


Theoretical massNumber of molelcules
Total (without water)70,1243
Polymers70,1243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-40 kcal/mol
Surface area29830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.289, 173.289, 140.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
12chain D
22chain F
32chain H
13chain E
23chain G
33chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GGCCchain AAA143 - 2481 - 68
21GGCCchain BBB143 - 2481 - 68
31GGCCchain CCC143 - 2481 - 68
12GLUGLULYSLYSchain DDD4 - 2254 - 225
22GLUGLULYSLYSchain FFF4 - 2254 - 225
32GLUGLULYSLYSchain HHH4 - 2254 - 225
13SERSERCYSCYSchain EEE1 - 2151 - 215
23SERSERCYSCYSchain GGG1 - 2151 - 215
33SERSERCYSCYSchain LLI1 - 2151 - 215

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 22014.154 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: JIIIabc of hepatitis C virus IRES / Source: (synth.) Hepacivirus C
#2: Antibody Heavy chain of Fab HCV3


Mass: 24698.537 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Heavy chain of Fab HCV3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Light chain of Fab HCV3


Mass: 23410.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Light chain of Fab HCV3 / 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.: 160 / 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: 5.01 Å3/Da / Density % sol: 75.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.75→173.289 Å / Num. obs: 106558 / % possible obs: 98.54 % / Redundancy: 4.7 % / CC1/2: 0.965 / Rmerge(I) obs: 0.1475 / Rpim(I) all: 0.07262 / Rrim(I) all: 0.165 / Net I/σ(I): 9.31
Reflection shellResolution: 2.75→2.848 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 10622 / CC1/2: 0.399 / Rpim(I) all: 0.5392 / % possible all: 99.03

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab HCV2, 6U8D

6u8d


Resolution: 2.75→173.289 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 2006 1.89 %
Rwork0.1864 104167 -
obs0.1871 106173 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 247.54 Å2 / Biso mean: 76.2683 Å2 / Biso min: 26.88 Å2
Refinement stepCycle: final / Resolution: 2.75→173.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9915 4380 0 160 14455
Biso mean---62.93 -
Num. residues----1515
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2439X-RAY DIFFRACTION9.641TORSIONAL
12B2439X-RAY DIFFRACTION9.641TORSIONAL
13C2439X-RAY DIFFRACTION9.641TORSIONAL
21D3057X-RAY DIFFRACTION9.641TORSIONAL
22F3057X-RAY DIFFRACTION9.641TORSIONAL
23H3057X-RAY DIFFRACTION9.641TORSIONAL
31E3052X-RAY DIFFRACTION9.641TORSIONAL
32G3052X-RAY DIFFRACTION9.641TORSIONAL
33L3052X-RAY DIFFRACTION9.641TORSIONAL
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 (%)
2.7501-2.81890.3761143740999
2.8189-2.89510.3613143746599
2.8951-2.98030.37051427521100
2.9803-3.07650.29281437470100
3.0765-3.18640.2819145747799
3.1864-3.3140.26011467452100
3.314-3.46490.2505140754499
3.4649-3.64760.2127146742599
3.6476-3.87610.1984143736798
3.8761-4.17540.19411420.1594738198
4.1754-4.59560.191410.1462749499
4.5956-5.26070.17011430.1454745198
5.2607-6.6280.1976144730496
6.6280.2152145740796
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)
12.6888-0.08620.6052.0984-0.33210.46240.11840.029-0.21380.1369-0.1699-0.06460.0162-0.24240.02280.69920.0775-0.2910.6184-0.03450.721314.811637.5275-25.6243
22.53110.55631.1392.65881.12711.9476-0.20190.1740.1251-0.11980.0092-0.0704-0.2076-0.12490.21690.69240.05110.01170.6648-0.19260.59248.407972.437322.4864
32.76740.5933-0.04393.05651.26210.5479-0.5981-0.6211-0.12910.95530.24360.08030.46340.20990.2291.00040.37680.28870.92090.09120.883383.915945.339755.966
43.7861-0.733-0.82942.44621.37891.83770.0655-0.27270.0404-0.0812-0.0983-0.0505-0.17650.00010.04940.2972-0.04180.01380.3439-0.01040.346680.623740.03213.2706
54.3298-1.14190.1642.84490.71841.41390.0690.0749-0.3575-0.2659-0.05110.13540.06820.02530.00860.4125-0.0385-0.00340.3134-0.02840.398472.960129.51260.892
63.9159-1.1926-1.72322.8710.35542.3840.004-0.1707-0.2756-0.08370.0467-0.07910.22240.3057-0.04190.42230.01430.02240.3128-0.03230.42842.857767.71964.2129
73.7938-0.1723-2.00151.15610.3222.082-0.1849-0.2567-0.68680.0931-0.0135-0.16020.50550.18210.06510.57830.07270.08620.44120.08330.724133.956256.527475.4119
81.8418-0.39111.05622.296-0.75661.9177-0.0046-0.0464-0.0854-0.30140.03150.06180.0871-0.21270.00210.46720.0028-0.05080.3234-0.03090.45947.83765.5596-15.7026
92.6541-1.5241.00314.1892-0.40071.5802-0.0828-0.18340.21650.06680.0409-0.3484-0.0107-0.0070.05660.302-0.0247-0.02660.3274-0.00720.40757.431914.1827-2.9415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA143 - 248
2X-RAY DIFFRACTION2Chain BB143 - 248
3X-RAY DIFFRACTION3Chain CC143 - 248
4X-RAY DIFFRACTION4Chain DD4 - 225
5X-RAY DIFFRACTION5Chain EE1 - 215
6X-RAY DIFFRACTION6Chain FF4 - 225
7X-RAY DIFFRACTION7Chain GG1 - 215
8X-RAY DIFFRACTION8Chain HH4 - 225
9X-RAY DIFFRACTION9Chain LL1 - 215

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