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- PDB-4hs8: Hepatitus C envelope glycoprotein E2 fragment 412-423 with humani... -

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Basic information

Entry
Database: PDB / ID: 4hs8
TitleHepatitus C envelope glycoprotein E2 fragment 412-423 with humanized and affinity-matured antibody hu5B3.v3
Components
  • (antibody hu5B3.v2 Fab ...) x 2
  • E2-peptide
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


host cell lipid droplet / lipid droplet / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Glycan shifting on hepatitis C virus (HCV) e2 glycoprotein is a mechanism for escape from broadly neutralizing antibodies.
Authors: Pantua, H. / Diao, J. / Ultsch, M. / Hazen, M. / Mathieu, M. / McCutcheon, K. / Takeda, K. / Date, S. / Cheung, T.K. / Phung, Q. / Hass, P. / Arnott, D. / Hongo, J.A. / Matthews, D.J. / ...Authors: Pantua, H. / Diao, J. / Ultsch, M. / Hazen, M. / Mathieu, M. / McCutcheon, K. / Takeda, K. / Date, S. / Cheung, T.K. / Phung, Q. / Hass, P. / Arnott, D. / Hongo, J.A. / Matthews, D.J. / Brown, A. / Patel, A.H. / Kelley, R.F. / Eigenbrot, C. / Kapadia, S.B.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E2-peptide
H: antibody hu5B3.v2 Fab heavy chain
L: antibody hu5B3.v2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6178
Polymers50,1493
Non-polymers4685
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-35 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.716, 77.716, 181.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide E2-peptide


Mass: 1727.877 Da / Num. of mol.: 1 / Fragment: UNP residues 50-62 / Source method: obtained synthetically
Details: This sequence occurs naturally in hepatitus C virus
Source: (synth.) Hepatitis C virus / References: UniProt: Q9YK84

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Antibody , 2 types, 2 molecules HL

#2: Antibody antibody hu5B3.v2 Fab heavy chain


Mass: 24653.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody antibody hu5B3.v2 Fab light chain


Mass: 23767.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsE2-PEPTIDE IS BIOTINYLATED, WITH BIOTIN (BTN) ATTACHED TO THE SIDE CHAIN OF THE C-TERMINAL LYS ...E2-PEPTIDE IS BIOTINYLATED, WITH BIOTIN (BTN) ATTACHED TO THE SIDE CHAIN OF THE C-TERMINAL LYS RESIDUE. HOWEVER, SOME RESIDUES AT THE C-TERMINUS, INCLUDING BTN, ARE MISSING DUE TO DISORDER.

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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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 17898 / Num. obs: 17880 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 73.69 Å2 / Rsym value: 0.098 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVC

1fvc


Resolution: 2.6→29.51 Å / Cor.coef. Fo:Fc: 0.9298 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.564 / Isotropic thermal model: TLS in 5 groups / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1024 5.74 %RANDOM
Rwork0.2223 ---
all0.225 18862 --
obs0.2246 17838 99.94 %-
Displacement parametersBiso mean: 65.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.195 Å20 Å20 Å2
2---1.195 Å20 Å2
3---2.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.441 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 28 26 3534
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.284884HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1182SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes519HARMONIC5
X-RAY DIFFRACTIONt_it3592HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion20.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion470SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3993SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.76 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3078 167 5.92 %
Rwork0.2497 2654 -
all0.2533 2821 -
obs--99.94 %
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)
12.46940.36560.53992.03470.88922.3021-0.03050.20640.3266-0.1780.0663-0.0122-0.2142-0.1215-0.0358-0.0656-0.08370.0399-0.0449-0.0055-0.00621.7532-10.6092-20.9329
22.8543-0.80521.50742.5215-1.64182.67450.1629-0.22390.05790.2365-0.2112-0.08420.06310.27870.0483-0.1473-0.1520.0310.1728-0.152-0.062823.818-10.62839.9719
32.9297-0.59780.34241.4523-0.09982.5104-0.22130.2333-0.3594-0.08070.12560.05370.49920.06650.09570.0466-0.10920.0684-0.1112-0.0806-0.03627.9834-31.2527-21.7111
41.0812-0.7175-0.47371.2904-0.87024.1040.0913-0.1959-0.01390.14680.00750.09260.2831-0.181-0.0987-0.1528-0.12720.02780.1524-0.056-0.081315.9156-23.751710.0761
501.2842-0.001100.59431.3753-0.00040.0363-0.0034-0.05030.0360.12690.033-0.0166-0.03560.0364-0.152-0.00730.1643-0.1265-0.1652-5.7745-26.1769-36.8313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ L|1 - L|107 }L1 - 107
2X-RAY DIFFRACTION2{ L|108 - L|214 }L108 - 214
3X-RAY DIFFRACTION3{ H|1 - H|113 }H1 - 113
4X-RAY DIFFRACTION4{ H|114 - H|216 }H114 - 216
5X-RAY DIFFRACTION5{ A|412 - A|423 }A412 - 423

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