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- PDB-8gbz: Crystal structure of PC39-55C, an anti-HIV broadly neutralizing a... -

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Basic information

Entry
Database: PDB / ID: 8gbz
TitleCrystal structure of PC39-55C, an anti-HIV broadly neutralizing antibody
Components
  • PC39-55C Fab heavy chain
  • PC39-55C Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Broadly Neutralizing / HIV-1 / V3 Glycan
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMurrell, S. / Omorodion, O. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationOPP119635 United States
CitationJournal: Plos Pathog. / Year: 2023
Title: Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies.
Authors: Joyce, C. / Murrell, S. / Murrell, B. / Omorodion, O. / Ver, L.S. / Carrico, N. / Bastidas, R. / Nedellec, R. / Bick, M. / Woehl, J. / Zhao, F. / Burns, A. / Barman, S. / Appel, M. / Ramos, ...Authors: Joyce, C. / Murrell, S. / Murrell, B. / Omorodion, O. / Ver, L.S. / Carrico, N. / Bastidas, R. / Nedellec, R. / Bick, M. / Woehl, J. / Zhao, F. / Burns, A. / Barman, S. / Appel, M. / Ramos, A. / Wickramasinghe, L. / Eren, K. / Vollbrecht, T. / Smith, D.M. / Kosakovsky Pond, S.L. / McBride, R. / Worth, C. / Batista, F. / Sok, D. / Poignard, P. / Briney, B. / Wilson, I.A. / Landais, E. / Burton, D.R.
History
DepositionFeb 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PC39-55C Fab heavy chain
L: PC39-55C Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2033
Polymers49,0972
Non-polymers1061
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-21 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.366, 171.380, 68.415
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody PC39-55C Fab heavy chain


Mass: 25507.467 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 PC39-55C Fab light chain


Mass: 23589.279 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium fluoride, 15% ethylene glycol, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 33396 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.03 / Rsym value: 0.09 / Net I/σ(I): 17.2
Reflection shellResolution: 1.97→2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1605 / CC1/2: 0.89 / Rpim(I) all: 0.25 / Rsym value: 0.59 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→43.85 Å / SU ML: 0.2663 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2184
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2648 1652 4.96 %
Rwork0.2188 31622 -
obs0.2211 33274 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.77 Å2
Refinement stepCycle: LAST / Resolution: 1.97→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 7 142 3499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493512
X-RAY DIFFRACTIONf_angle_d0.74364798
X-RAY DIFFRACTIONf_chiral_restr0.0479536
X-RAY DIFFRACTIONf_plane_restr0.0054621
X-RAY DIFFRACTIONf_dihedral_angle_d15.89731267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.33281360.34132478X-RAY DIFFRACTION96.32
2.03-2.10.41171290.32392598X-RAY DIFFRACTION98.98
2.1-2.170.36231250.29412610X-RAY DIFFRACTION99.27
2.17-2.260.38261340.29472592X-RAY DIFFRACTION99.31
2.26-2.360.29141420.27162611X-RAY DIFFRACTION99.53
2.36-2.480.3111220.26642629X-RAY DIFFRACTION98.96
2.48-2.640.32451450.27942624X-RAY DIFFRACTION99.18
2.64-2.840.33091460.26152627X-RAY DIFFRACTION99.6
2.84-3.130.29471480.23922620X-RAY DIFFRACTION99.53
3.13-3.580.27071400.21542702X-RAY DIFFRACTION99.47
3.58-4.510.19321400.17342683X-RAY DIFFRACTION99.61
4.51-43.850.21771450.16912848X-RAY DIFFRACTION99.07
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)
14.15689731758-0.7629763031530.3738991326456.65385670622-0.09258135089934.91948145902-0.03594789865050.4757292623190.0560777269504-0.371628690806-0.015920042023-0.3442761874380.258874488202-0.275305326084-0.02000404024410.584522058152-0.0408077402512-0.03725054186790.282601062494-0.0358859250550.2926396154862.491-28.537-12.081
24.04210821283-1.069416150960.4066871182156.83431185269-0.6080276397044.409139381-0.1105172509470.08620882779250.385507830301-0.0475420324277-0.0221930419421-1.01225266037-0.3964373771570.1811920843150.1304729915580.490480366611-0.0456067262782-0.09591992760230.21296150928-0.01503706261910.4425080394377.151-22.077-8.345
30.9051932981950.206631445391-1.224288842450.945705414315-1.222269991013.3596084215-0.226469603254-0.119933311346-0.0103875221535-0.2496027784630.02878553388050.09246741559650.5859529878710.237723641780.11197722220.4856288359380.00836377344882-0.1014812076110.278791002892-0.06753285137850.301213913153-8.631-32.7912.399
46.8252289967-3.41489602297-1.961087893815.242909562721.61828487353.28058026995-0.0116230363413-0.0207159172237-0.308423613593-0.86794117281-0.1536679629820.7614298138830.0751066556004-0.1916201991460.1754085469650.5671352947990.0251753531736-0.1337498382520.239843700999-0.01936483202220.34567026907-18.644-34.83818.412
53.105713883420.691855908756-2.245165397917.34189553024-0.5424562288623.85777728052-0.03295510176220.05234481648580.4847536696450.6144847186990.0723072622464-0.306301253925-0.534354284046-0.114180837053-0.0502779677460.5529446416890.0236503845676-0.1975231053030.2442878047220.04899291503830.400656989029-5.623-5.164-3.774
62.748296641310.0410962688201-2.963249210741.73880202187-1.190906073954.694678647450.1537563415070.1255736608190.258968902340.408290153809-0.0387507628362-0.173927793827-0.768044591733-0.212116601949-0.2522701444090.6297087301920.0512960255992-0.140777324710.236371532795-0.01941696912320.449478566721-7.412-102.468
74.62720481323-2.815076303452.214296207575.22422179619-2.182456290965.420626727160.171791448011-0.1096655823760.0933998471598-0.4571610009-0.1833832867090.0391430576748-0.01197864724860.365066572109-0.02704871298830.2812672719880.002317470332940.06449194919850.254061949491-0.09689984966520.270945011206-9.491-24.81727.864
83.46685520793-3.222989870882.152766672557.30627103927-3.326881053145.52303979560.0899683165689-0.1421346970960.218961481920.1162046344790.05890104640290.0193381627279-0.246564156190.101609135906-0.1657507829080.296621205696-0.04864444095360.0484704878220.240155428506-0.07400742403870.289646210461-11.362-22.72629.651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:31 )H1 - 31
2X-RAY DIFFRACTION2( CHAIN H AND RESID 32:100 )H32 - 100
3X-RAY DIFFRACTION3( CHAIN H AND RESID 101:145 )H101 - 145
4X-RAY DIFFRACTION4( CHAIN H AND RESID 146:215 )H146 - 215
5X-RAY DIFFRACTION5( CHAIN L AND RESID 2:76 )L2 - 76
6X-RAY DIFFRACTION6( CHAIN L AND RESID 77:113 )L77 - 113
7X-RAY DIFFRACTION7( CHAIN L AND RESID 114:163 )L114 - 163
8X-RAY DIFFRACTION8( CHAIN L AND RESID 164:214 )L164 - 214

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