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- PDB-8gc0: Crystal structure of PC39-50L, an anti-HIV broadly neutralizing a... -

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Basic information

Entry
Database: PDB / ID: 8gc0
TitleCrystal structure of PC39-50L, an anti-HIV broadly neutralizing antibody
Components
  • PC39-50L Fab heavy chain
  • PC39-50L Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Broadly Neutralizing / HIV-1 / V3 Glycan
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: PC39-50L Fab heavy chain
L: PC39-50L Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3183
Polymers49,0972
Non-polymers2211
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-24 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.810, 69.219, 81.643
Angle α, β, γ (deg.)90.000, 94.276, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody PC39-50L Fab heavy chain


Mass: 25602.635 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 PC39-50L Fab light chain


Mass: 23493.990 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.085 M sodium acetate pH 4.6, 0.17 M ammonium acetate, 15% glycerol, 25.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 16654 / % possible obs: 98.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 34.23 Å2 / CC1/2: 0.88 / Rpim(I) all: 0.08 / Rsym value: 0.17 / Net I/σ(I): 11.2
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 761 / CC1/2: 0.75 / Rpim(I) all: 0.32 / Rsym value: 0.61 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→40.71 Å / SU ML: 0.3503 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2519 808 4.9 %
Rwork0.2114 15667 -
obs0.2133 16475 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.1 Å2
Refinement stepCycle: LAST / Resolution: 2.43→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 14 82 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223541
X-RAY DIFFRACTIONf_angle_d0.53814828
X-RAY DIFFRACTIONf_chiral_restr0.0435539
X-RAY DIFFRACTIONf_plane_restr0.0046621
X-RAY DIFFRACTIONf_dihedral_angle_d15.1461269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.580.35331350.30752411X-RAY DIFFRACTION91.71
2.58-2.780.32211300.28272606X-RAY DIFFRACTION98.45
2.78-3.060.30941650.25812627X-RAY DIFFRACTION99.22
3.06-3.50.24641120.21492648X-RAY DIFFRACTION99.32
3.5-4.410.21311380.1782665X-RAY DIFFRACTION99.61
4.41-40.710.20551280.17522710X-RAY DIFFRACTION99.72
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)
12.706590687690.148020419913-0.7343817668663.85238167860.4315433949563.30151065104-0.196290919731-0.0512172225343-0.1725646983120.02430818431470.133836132520.00301305241163-0.17105743887-0.1192110187250.07889842609110.3435509418850.0210182108384-0.05300810577890.2324849821630.02324777703610.26296308708216.1524127863-24.11587959328.2717517171
22.01275925683-1.97153789831-1.108258511744.262599003311.734053632373.8321880143-0.0250597959072-0.114094499383-0.186648024468-0.0251422741463-0.0760824336779-0.0587111274336-0.394308664103-0.06070939648350.0766545191060.33477046001-0.00498032474051-0.05492092520860.2081108452580.04057600689940.34067944481718.244895813-26.188334161726.0809808009
31.79113035059-1.609333275111.55373503723.55240683363-0.1360079483233.0465999356-0.0841652115124-0.0213684325234-0.1353712049750.6017401163690.01953463295510.0903935305241-0.08538448213540.310765787430.06576899204510.175262467871-0.005297658623190.05701380362240.2178928550680.02053157282470.2784615776570.4062592621334.5344180079227.3459902831
42.40374064517-0.07674150697220.07490715925474.7378594705-1.047614192962.970349635060.0831626835137-0.0368160442645-0.2673804648710.202817973635-0.05630993978120.2496802728870.03982166793870.06065194255380.007159505297390.161141664038-0.0160961582684-0.01215782876980.1819369571620.02415156343640.225837732695-3.486810097374.8764252505922.3588238522
54.94056174207-1.895660775581.704337857135.67939006705-2.127188093554.2555900559-0.113740972946-0.49993967556-0.1926294714390.4320825895390.3623136224371.10288764109-0.298389818791-0.303171990082-0.2051527726870.2100060342940.02739727989870.08042777630740.2496970684240.007705213850170.403871564518-11.28481946278.0719677284126.353872492
63.8685620518-1.326732575912.983380162436.26998651472-2.411314662414.649390937950.1027156780610.320759152284-0.0862746393777-0.468576122127-0.442004068275-0.2493867727980.06588048792550.49638006190.3899744349080.359687973765-0.03007145331290.04542856966010.2459186948220.03026947259530.31003141304318.6038703056-9.021612878893.76489749213
75.07355172401-1.901941569393.852421418056.43157656999-2.577328006853.968337953980.348021391920.6221173938950.629934459176-0.129065334443-0.511796976966-1.30706226279-0.3671205451690.7680942435830.7635436716750.4277706499990.02688430287770.2168068921840.3654122434480.1080900144180.61520176104528.8266029295-14.52792007017.42747359058
81.57818163208-1.587694292180.7431621773565.11103220467-2.443562873591.954517430280.1778664815640.191544538977-0.290299004004-0.571612812942-0.2204939827440.00538106344110.1254342663810.1916803404470.05672900275220.345060833680.04318670193860.01986406721430.260941356747-0.01012700799130.2284558158616.886446707-16.74927495447.55339042714
90.4194195514070.5729903745991.250641779073.619901823171.784497095017.543672462760.0667874188971-0.00412522278420.04582812887640.2079442870420.0720927643509-0.1719194465450.32760978381-0.057977842879-0.1226622932020.193359904431-0.00317377371435-0.01431172973940.16566352962-0.006966600353390.2885999139915.5156318893712.901208486620.1307863332
102.3159027809-0.0661334047369-0.2059157490646.859674260141.752599048562.120284582280.0691001954595-0.3890295405020.2386309764580.505427443997-0.254775260475-0.1664367616730.0782097366397-0.1337233803630.1514737400170.2109143756050.00571193002183-0.01893552762740.3052414606410.009477116512870.3093440835914.375170831612.760622259223.6329950256
111.650695575681.268811814722.177753675784.130591448093.593266004616.368754650320.1214158526520.00368009219306-0.1706123821790.06295869983240.187509147229-0.2699230606540.17865183677-0.00237434050937-0.2614929541170.181509390974-0.00427358084974-0.01565381554790.179288299950.03267310516030.3053872914057.2549732368911.938829774119.5531273802
121.779279483471.772706555122.00776305975.516952033575.0337586199.92995852788-0.625981661723-0.433931594449-0.0694620723657-1.29314388750.1928215606460.12706307545-1.26447234077-0.5837345377920.08461726654280.459381669646-0.08981175972180.07759197035240.04744071647010.002022806689470.5085914240947.6711514728421.798503012415.3722557948
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 63 )HA1 - 631 - 67
22chain 'H' and (resid 64 through 104 )HA64 - 10468 - 123
33chain 'H' and (resid 105 through 134 )HA105 - 134124 - 153
44chain 'H' and (resid 135 through 190 )HA135 - 190154 - 209
55chain 'H' and (resid 191 through 216 )HA191 - 216210 - 235
66chain 'L' and (resid 2 through 18 )LC2 - 181 - 17
77chain 'L' and (resid 19 through 29 )LC19 - 2918 - 29
88chain 'L' and (resid 30 through 113 )LC30 - 11330 - 114
99chain 'L' and (resid 114 through 150 )LC114 - 150115 - 151
1010chain 'L' and (resid 151 through 163 )LC151 - 163152 - 164
1111chain 'L' and (resid 164 through 198 )LC164 - 198165 - 199
1212chain 'L' and (resid 199 through 214 )LC199 - 214200 - 215

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