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- PDB-7ssc: TRL345 lineage ancestor I8 Fab bound to an HCMV gB-derived peptide -

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Basic information

Entry
Database: PDB / ID: 7ssc
TitleTRL345 lineage ancestor I8 Fab bound to an HCMV gB-derived peptide
Components
  • Envelope glycoprotein B peptide
  • TRL345-I8 Fab heavy chain
  • TRL345-I8 Fab light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / immunoglobulin / fusion protein / HCMV / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / : / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain ...Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / : / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHomo sapiens (human)
Human betaherpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSponholtz, M.R. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: Plos Pathog. / Year: 2023
Title: A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus.
Authors: Jenks, J.A. / Amin, S. / Sponholtz, M.R. / Kumar, A. / Wrapp, D. / Venkatayogi, S. / Tu, J.J. / Karthigeyan, K. / Valencia, S.M. / Connors, M. / Harnois, M.J. / Hora, B. / Rochat, E. / ...Authors: Jenks, J.A. / Amin, S. / Sponholtz, M.R. / Kumar, A. / Wrapp, D. / Venkatayogi, S. / Tu, J.J. / Karthigeyan, K. / Valencia, S.M. / Connors, M. / Harnois, M.J. / Hora, B. / Rochat, E. / McLellan, J.S. / Wiehe, K. / Permar, S.R.
History
DepositionNov 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: 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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: TRL345-I8 Fab heavy chain
L: TRL345-I8 Fab light chain
P: Envelope glycoprotein B peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7604
Polymers48,6683
Non-polymers921
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-31 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.879, 74.669, 104.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody TRL345-I8 Fab heavy chain


Mass: 23568.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody TRL345-I8 Fab light chain


Mass: 23315.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Envelope glycoprotein B peptide / 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 54.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M magnesium chloride hexahydrate, 25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→66.88 Å / Num. obs: 48200 / % possible obs: 97.9 % / Redundancy: 6 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.028 / Rrim(I) all: 0.07 / Net I/σ(I): 17.2 / Num. measured all: 287280 / Scaling rejects: 175
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8460.1391700128260.9820.0620.1539.698
9-66.885.90.03627664690.9980.0160.03923.599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UOE, 6ZFO

6uoe

6zfo


Resolution: 1.8→56.39 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1742 2377 4.94 %
Rwork0.1503 45764 -
obs0.1515 48141 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.62 Å2 / Biso mean: 18.1973 Å2 / Biso min: 4.88 Å2
Refinement stepCycle: final / Resolution: 1.8→56.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 6 723 4090
Biso mean--14 31.71 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.2071570.17912634279198
1.84-1.880.2011560.16292650280698
1.88-1.920.18411500.1552640279097
1.92-1.970.19561090.14932607271694
1.97-2.020.20081280.1452686281498
2.02-2.080.18851350.14482668280398
2.08-2.150.171460.1462694284099
2.15-2.230.15561390.14192709284899
2.23-2.310.17271540.14382658281298
2.31-2.420.1871330.15372605273895
2.42-2.550.19861200.15952761288199
2.55-2.710.18731140.15842732284698
2.71-2.920.20211470.15992750289799
2.92-3.210.17221350.15422612274794
3.21-3.670.13921430.13762775291899
3.67-4.630.14161530.13382696284995
4.63-56.390.18441580.16352887304598
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)
10.86370.80360.08841.4405-0.02740.2374-0.0041-0.02120.0021-0.0370.01550.06590.015-0.0139-0.01150.04230.0129-0.00750.08510.0040.0503-16.6242-32.4211.7042
20.42890.534-0.02471.51610.10120.0250.0477-0.0323-0.01470.0469-0.06220.00910.02460.02270.02190.07490.0067-0.02130.09770.00870.0424-8.8502-42.860414.4655
35.30710.7174-1.76064.8032-0.52737.77590.0033-0.20780.3430.26740.04230.1272-0.2998-0.1666-0.06550.062-0.0021-0.01480.0511-0.02470.08021.8257-8.762210.7589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain HH1 - 213
2X-RAY DIFFRACTION2chain LL1 - 213
3X-RAY DIFFRACTION3chain PP69 - 79

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