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- PDB-8gbw: Crystal structure of PC39-23D, an anti-HIV broadly neutralizing a... -

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Basic information

Entry
Database: PDB / ID: 8gbw
TitleCrystal structure of PC39-23D, an anti-HIV broadly neutralizing antibody
Components
  • PC39-23D Fab heavy chain
  • PC39-23D Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Broadly Neutralizing / HIV-1 / V3 Glycan
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
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 / _pdbx_validate_planes.type
Revision 1.2Aug 16, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type
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: PC39-23D Fab heavy chain
L: PC39-23D Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,14616
Polymers50,1452
Non-polymers1,00114
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint9 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.284, 83.367, 151.767
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 PC39-23D Fab heavy chain


Mass: 26221.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal pyroglutamic acid residue is a post-translationally modified Gln
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PC39-23D Fab light chain


Mass: 23923.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal residues "VH" originate from the signal peptide
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 98412 / % possible obs: 99.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.96 / Rpim(I) all: 0.03 / Rsym value: 0.11 / Net I/σ(I): 22.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4847 / CC1/2: 0.81 / Rpim(I) all: 0.39 / Rsym value: 1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→36.53 Å / SU ML: 0.1373 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 4911 4.99 %
Rwork0.1816 93413 -
obs0.1826 98324 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.94 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 65 430 4006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01314156
X-RAY DIFFRACTIONf_angle_d1.335703
X-RAY DIFFRACTIONf_chiral_restr0.0858630
X-RAY DIFFRACTIONf_plane_restr0.0136753
X-RAY DIFFRACTIONf_dihedral_angle_d16.87961528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.27071520.22992983X-RAY DIFFRACTION96.02
1.52-1.540.22461590.22293064X-RAY DIFFRACTION99.44
1.54-1.550.25611630.21873072X-RAY DIFFRACTION99.08
1.55-1.570.231390.20993048X-RAY DIFFRACTION98.39
1.57-1.590.25641490.20073052X-RAY DIFFRACTION98.89
1.59-1.620.20611620.18773103X-RAY DIFFRACTION99.88
1.62-1.640.18931630.18583096X-RAY DIFFRACTION99.91
1.64-1.660.17641550.18593107X-RAY DIFFRACTION99.82
1.66-1.690.18681630.18433065X-RAY DIFFRACTION100
1.69-1.720.20451470.18393128X-RAY DIFFRACTION99.91
1.72-1.750.20231680.19163099X-RAY DIFFRACTION99.63
1.75-1.780.2251850.19623080X-RAY DIFFRACTION99.88
1.78-1.810.20371510.19663108X-RAY DIFFRACTION99.76
1.81-1.850.21571720.193106X-RAY DIFFRACTION99.73
1.85-1.890.18561540.17813085X-RAY DIFFRACTION99.48
1.89-1.930.21611630.17693097X-RAY DIFFRACTION99.33
1.93-1.980.2081680.17493034X-RAY DIFFRACTION98.67
1.98-2.040.18521750.18033108X-RAY DIFFRACTION99.79
2.04-2.10.18951630.17833168X-RAY DIFFRACTION100
2.1-2.160.19671610.18123074X-RAY DIFFRACTION99.94
2.16-2.240.21951720.18413113X-RAY DIFFRACTION99.79
2.24-2.330.1991670.19433130X-RAY DIFFRACTION99.64
2.33-2.440.2311780.19143117X-RAY DIFFRACTION100
2.44-2.570.2211740.19013150X-RAY DIFFRACTION100
2.57-2.730.21931670.19833134X-RAY DIFFRACTION99.64
2.73-2.940.18361600.20093133X-RAY DIFFRACTION98.8
2.94-3.230.20461490.18863206X-RAY DIFFRACTION99.97
3.23-3.70.22751750.17263186X-RAY DIFFRACTION99.61
3.7-4.660.15961650.14943198X-RAY DIFFRACTION99.23
4.66-36.530.1771920.16113369X-RAY DIFFRACTION99.55
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)
11.76944136475-0.8615183716122.014594815585.47541217484-5.259424378547.578891721060.110897015640.0131242489226-0.197019033315-0.3730101490140.2267871214310.4203134023660.393651290576-0.392680355359-0.3467753267530.08565043171360.00332984605672-0.01660539373030.100377647196-0.02897271729570.109363613044-26.310105876915.0135609132-19.2342709786
20.952280878907-0.1485808043150.7128720493310.738692654052-0.6861644495121.998118307330.0265775597256-0.00575182955997-0.05139046354130.0056879554323-0.001248790520660.04061495374850.0312834056859-0.0497438092809-0.02563198606180.06862217160890.00992302969049-0.0002268303997080.0659195898226-0.0128664823860.0836711277516-16.485594678516.5125993529-7.63391172522
30.510052833550.343966624659-0.8619343662952.58723036718-2.757180524487.840051593790.1026941329780.04061121715410.07679145335460.06180407736220.08214583618050.178635958215-0.0853839383953-0.377809735714-0.1763678860150.04603592599390.00598323161499-0.007943157679650.0901510286942-0.01115198629340.113051487077-24.10191782219.1360758444-11.4876258163
41.61186819876-0.3829660788542.489655021220.234103757095-0.5568321632465.563640829610.149705455821-0.0394518722898-0.0953024252605-0.0549982611205-0.0607305558050.07004739534060.293042112307-0.102075042649-0.09128416867860.102651882566-0.000262666182915-0.009793636088870.0620016263123-0.01262450385430.105455030148-14.79884496169.9190747576-11.1249152222
51.23962907862-0.688440402303-0.833111191521.393203539021.245214589852.95374512846-0.00671985617135-0.07382139922340.172610236021-0.05507947189680.0780392368659-0.0842130889006-0.1130564165830.00256544398999-0.0671304465510.0861543640792-0.0156356055878-0.01002910907130.0895692821583-0.02350574646460.112310593424-17.95491515473.96339156195-46.7064501674
66.24671696533-5.91197907814-7.173036586916.103653611897.006167483918.93259314661-0.149669480066-0.0527788962533-0.04958981808430.084040298715-0.04958432372190.1663620787240.151109399557-0.117045390030.1816996599240.0921022158833-0.03589992842110.004577537472890.129298664066-0.03882513380040.121880466263-25.5360952664-1.6646709036-45.9025487125
72.15581246-1.54039774477-7.954135152292.79535665452.239833956128.44485663105-0.3839697632090.6368738169840.0935336088484-0.250413085189-0.1077280514240.2866969229670.0970619047246-1.062165535610.3957061142990.127915481083-0.0436649803582-0.05536807784910.400173662026-0.05429775561980.163524438986-26.6773967681.45901781987-51.7237593157
81.2653883593-0.103158503369-0.310854319643.321518539842.557190769043.759248806220.08391591195780.336553911079-0.0380890994928-0.2069700194370.0177392607943-0.0713222063059-0.1328573440670.344392402801-0.110382449280.08177250502570.0326225185095-0.001814687478960.181896526143-0.03572411597710.09251633594734.9038143469413.8570813527-18.3788006797
90.4817318761610.0229407659817-0.2610651768720.3084453864580.4358533036921.88405063680.02314447327430.104446048648-0.1597180915810.04039624560310.0372475960534-0.06978842633370.2602316517940.158105608082-0.04883544531050.1048774384330.0385215581893-0.02616372894710.115465446869-0.04323892732120.128521512095-0.1032085022255.51199144032-16.1941751575
102.302602135-1.250457617940.6358519419922.72390942266-0.7924642047983.00301717306-0.1561739470690.2828489236420.4102505289820.03332862054190.0360552268641-0.128712780659-0.4078738761520.06801902226230.1044384359020.146339115308-0.022385931846-0.003727108602130.1144013887280.01847973942630.160915775497-11.170812586811.7051767092-49.4800278854
111.98768425835-0.9029083820560.7423291706331.26191025099-0.283126990691.77817076092-0.1129897280770.3009316539940.5902458417350.00737608195652-0.0956326455547-0.261334320671-0.4697866950250.2389656736650.1670002267720.206651947015-0.0562104649293-0.0238199973490.1590036697520.05754358066080.29847427577-7.8636289532314.204609752-49.5562787077
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 2 through 17 )HA2 - 172 - 17
22chain 'H' and (resid 18 through 66 )HA18 - 6618 - 77
33chain 'H' and (resid 67 through 87 )HA67 - 8778 - 101
44chain 'H' and (resid 88 through 119 )HA88 - 119102 - 145
55chain 'H' and (resid 120 through 190 )HA120 - 190146 - 216
66chain 'H' and (resid 191 through 203 )HA191 - 203217 - 229
77chain 'H' and (resid 204 through 215 )HA204 - 215230 - 241
88chain 'L' and (resid -1 through 29 )LB-1 - 291 - 32
99chain 'L' and (resid 30 through 113 )LB30 - 11333 - 117
1010chain 'L' and (resid 114 through 150 )LB114 - 150118 - 154
1111chain 'L' and (resid 151 through 213 )LB151 - 213155 - 217

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