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- PDB-6uoe: 3-25 Fab germline-reversion variant bound to an HCMV gB-derived p... -

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Basic information

Entry
Database: PDB / ID: 6uoe
Title3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
Components
  • 3-25 Fab heavy chain
  • 3-25 Fab light chain
  • Envelope glycoprotein B
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / fragment antigen-binding / viral peptide / HCMV gB / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell Golgi membrane / immunoglobulin complex / host cell endosome membrane / adaptive immune response / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region ...host cell Golgi membrane / immunoglobulin complex / host cell endosome membrane / adaptive immune response / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Immunoglobulin V-Type ...Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Envelope glycoprotein B / Immunoglobulin gamma-1 heavy chain / Immunoglobulin kappa light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Human betaherpesvirus 5
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWrapp, D. / McLellan, J.S.
CitationJournal: Plos Pathog. / Year: 2020
Title: Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step.
Authors: Ye, X. / Su, H. / Wrapp, D. / Freed, D.C. / Li, F. / Yuan, Z. / Tang, A. / Li, L. / Ku, Z. / Xiong, W. / Jaijyan, D. / Zhu, H. / Wang, D. / McLellan, J.S. / Zhang, N. / Fu, T.M. / An, Z.
History
DepositionOct 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
H: 3-25 Fab heavy chain
L: 3-25 Fab light chain
P: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9085
Polymers49,6803
Non-polymers2282
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-26 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.663, 67.587, 84.031
Angle α, β, γ (deg.)90.000, 133.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-498-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Envelope glycoprotein B / gB / gB-p17


Mass: 1783.959 Da / Num. of mol.: 1 / Fragment: antigenic domain-2 (UNP residues 65-79) / Source method: obtained synthetically / Source: (synth.) Human betaherpesvirus 5 / References: UniProt: P06473

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Antibody , 2 types, 2 molecules HL

#1: Antibody 3-25 Fab heavy chain


Mass: 24382.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Antibody 3-25 Fab light chain


Mass: 23514.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7

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Non-polymers , 3 types, 648 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M magnesium chloride, 13.4% PEG3350, 16.75% PEG400, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→33.32 Å / Num. obs: 41589 / % possible obs: 92.1 % / Redundancy: 2.5 % / CC1/2: 0.995 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3 / Num. unique obs: 2525 / CC1/2: 0.91 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
MOSFLM7.2.2data reduction
Aimless1.11.19data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 6BLA & 6DDM

6bla

6ddm


Resolution: 1.8→33.319 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.24
RfactorNum. reflection% reflection
Rfree0.1858 2096 5.05 %
Rwork0.1604 --
obs0.1617 41535 92.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.27 Å2 / Biso mean: 22.3803 Å2 / Biso min: 8.44 Å2
Refinement stepCycle: final / Resolution: 1.8→33.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 15 646 4091
Biso mean--36.28 35.23 -
Num. residues----451
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.84190.35071690.2776268697
1.8419-1.8880.25941090.2234276196
1.888-1.9390.18871530.181270796
1.939-1.9960.19071230.1626272195
1.996-2.06050.18831570.1619270395
2.0605-2.13410.19061460.1692262093
2.1341-2.21950.19621560.1604262893
2.2195-2.32050.20751230.1584265093
2.3205-2.44280.1851430.1608262892
2.4428-2.59580.19331400.1647259691
2.5958-2.79610.17161500.1587256891
2.7961-3.07740.18191240.1577259290
3.0774-3.52220.15481400.1487255390
3.5222-4.4360.17151140.1371256989
4.436-33.30.17811490.1544245784
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)
11.39160.36990.19351.78131.47862.70730.0334-0.013-0.06240.02360.1308-0.31350.14960.0453-0.14230.13470.0196-0.00890.12330.03380.1723.5506-29.058429.5116
21.380.1525-0.0031.43150.171.6508-0.0156-0.0803-0.14210.02610.0033-0.1170.0126-0.08270.02270.09720.00650.01530.09930.00920.129515.2301-30.93331.5302
30.771-0.5244-0.91652.04861.01462.6427-0.0132-0.0055-0.076-0.1305-0.0238-0.05290.091-0.14720.03020.12180.00720.01190.13660.00740.156615.3856-30.148623.6982
42.94471.0447-0.66724.5851.01131.17370.1577-0.5618-0.06550.5889-0.02850.12490.12280.18680.03340.19930.005-0.00210.21710.02080.155812.0868-22.103745.007
50.7407-0.6131-0.87180.66211.12823.17550.00580.0005-0.0223-0.0044-0.04660.02590.02680.06360.010.1422-0.00640.01170.14420.00980.146120.8878-28.045217.7154
61.68790.7763-0.1730.57520.511.42090.13330.22760.4072-0.9221-0.01640.37390.09210.021-0.16580.28790.0136-0.06350.22620.0720.243321.4589-16.5532-14.1008
70.17010.6517-0.53124.7531-2.43882.30830.04340.0710.04070.0059-0.02920.04990.00520.115-0.05550.1118-0.0058-0.01290.17070.02270.153723.9162-19.958-2.3005
80.37491.1035-1.12057.4748-4.61953.52060.02410.0216-0.0747-0.2191-0.3834-0.54430.15620.34270.36210.1350.03210.02460.23320.04790.221932.6075-21.3197-6.645
91.42240.5819-1.0722.3853-1.41232.41650.0560.03020.1329-0.00240.07910.1366-0.0852-0.0161-0.13460.10790.00890.00650.1077-0.01380.11632.8467-10.333824.6922
101.11510.0043-0.53052.1446-0.81621.90460.0417-0.02390.1275-0.0277-0.0043-0.1438-0.11310.1509-0.03120.0876-0.01290.00550.1243-0.01590.12318.8091-9.771528.1204
110.03220.1118-0.39230.5758-1.74235.44050.07490.1158-0.1180.1151-0.02430.2212-0.49460.11890.01470.1879-0.00120.02690.16950.00320.14639.8334-2.73455.5034
122.1876-0.99630.30978.31441.87893.61310.22850.2843-0.1282-0.4474-0.0725-0.41850.17460.448-0.41860.17540.0269-0.01620.2489-0.01740.16719.0048-23.7234-14.373
130.32970.91490.5926.30824.00134.0433-0.0626-0.02440.04150.1960.03720.27250.1816-0.00730.05130.14520.0159-0.00140.15650.02090.11949.4479-15.5501-5.7254
141.34820.83571.42323.1022.29564.1860.2583-0.274-0.11980.2821-0.00540.05130.3571-0.56610.09170.1467-0.04690.00760.18360.04720.13945.4174-23.639-7.8169
151.14250.25980.63075.09993.32464.10980.15680.0129-0.07410.0872-0.02230.01240.1448-0.0105-0.17690.1085-0.0142-0.00280.14030.01180.125211.8061-19.0934-7.9042
161.5239-0.47030.30986.57294.22195.10890.0623-0.03880.0214-0.4959-0.0880.2022-0.35510.015-0.01440.16280.0076-0.02920.14530.00730.13697.6637-12.8577-14.8087
178.44191.692-0.51896.7267-0.94085.8492-0.1624-0.44990.44850.44090.17480.2351-0.05760.09510.11390.16350.034-0.02120.1904-0.03580.03611.0526-19.40844.5041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 33 )H2 - 33
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 82 )H34 - 82
3X-RAY DIFFRACTION3chain 'H' and (resid 82A through 95 )H82
4X-RAY DIFFRACTION4chain 'H' and (resid 96 through 100G)H96 - 100
5X-RAY DIFFRACTION5chain 'H' and (resid 100H through 119 )H100
6X-RAY DIFFRACTION6chain 'H' and (resid 120 through 134 )H120 - 134
7X-RAY DIFFRACTION7chain 'H' and (resid 135 through 188 )H135 - 188
8X-RAY DIFFRACTION8chain 'H' and (resid 189 through 213 )H189 - 213
9X-RAY DIFFRACTION9chain 'L' and (resid 1 through 38 )L1 - 38
10X-RAY DIFFRACTION10chain 'L' and (resid 39 through 102 )L39 - 102
11X-RAY DIFFRACTION11chain 'L' and (resid 103 through 113 )L103 - 113
12X-RAY DIFFRACTION12chain 'L' and (resid 114 through 128 )L114 - 128
13X-RAY DIFFRACTION13chain 'L' and (resid 129 through 150 )L129 - 150
14X-RAY DIFFRACTION14chain 'L' and (resid 151 through 163 )L151 - 163
15X-RAY DIFFRACTION15chain 'L' and (resid 164 through 197 )L164 - 197
16X-RAY DIFFRACTION16chain 'L' and (resid 198 through 213 )L198 - 213
17X-RAY DIFFRACTION17chain 'P' and (resid 68 through 79 )P68 - 79

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