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- PDB-6dc4: RSV-neutralizing human antibody AM22 -

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Basic information

Entry
Database: PDB / ID: 6dc4
TitleRSV-neutralizing human antibody AM22
Components
  • Fab AM22 Heavy Chain
  • Fab AM22 Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Fab
Function / homology
Function and homology information


extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IGH@ protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJones, H.G. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: Plos Pathog. / Year: 2019
Title: Alternative conformations of a major antigenic site on RSV F.
Authors: Jones, H.G. / Battles, M.B. / Lin, C.C. / Bianchi, S. / Corti, D. / McLellan, J.S.
History
DepositionMay 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: 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 1.3Oct 4, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab AM22 Heavy Chain
L: Fab AM22 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,45219
Polymers47,3972
Non-polymers1,05517
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint22 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.240, 75.220, 109.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab AM22 Heavy Chain


Mass: 24123.217 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: Q6GMX6
#2: Antibody Fab AM22 Light Chain


Mass: 23273.938 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: Q8TCD0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 0.1 M MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→32.72 Å / Num. obs: 58786 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 20172 / CC1/2: 0.714 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
Aimless0.7.1data scaling
PHASER2.8.0phasing
PHENIX1.12_2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LMJ, 3QEG

3lmj

3qeg


Resolution: 1.7→32.72 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.77
RfactorNum. reflection% reflection
Rfree0.2049 1999 3.41 %
Rwork0.1804 --
obs0.1812 58706 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 68 596 3955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063419
X-RAY DIFFRACTIONf_angle_d0.8364619
X-RAY DIFFRACTIONf_dihedral_angle_d18.651228
X-RAY DIFFRACTIONf_chiral_restr0.058529
X-RAY DIFFRACTIONf_plane_restr0.005584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.74350.31191380.27593976X-RAY DIFFRACTION100
1.7435-1.79070.26791430.24554029X-RAY DIFFRACTION100
1.7907-1.84340.22871410.22123998X-RAY DIFFRACTION100
1.8434-1.90290.24211400.20673988X-RAY DIFFRACTION100
1.9029-1.97090.22791420.19913999X-RAY DIFFRACTION100
1.9709-2.04980.22581410.19174015X-RAY DIFFRACTION100
2.0498-2.1430.21211420.18584033X-RAY DIFFRACTION100
2.143-2.2560.21621420.17744017X-RAY DIFFRACTION100
2.256-2.39730.20121430.18134028X-RAY DIFFRACTION100
2.3973-2.58230.18561440.17974066X-RAY DIFFRACTION100
2.5823-2.84210.20771420.18154034X-RAY DIFFRACTION100
2.8421-3.2530.17571440.17614100X-RAY DIFFRACTION100
3.253-4.09720.17561460.15524129X-RAY DIFFRACTION100
4.0972-32.72510.21251510.16524295X-RAY DIFFRACTION100

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