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

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Basic information

Entry
Database: PDB / ID: 8gbx
TitleCrystal structure of PC39-50I, an anti-HIV broadly neutralizing antibody
Components
  • PC39-50I Fab heavy chain
  • PC39-50I 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: 2.7 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 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: PC39-50I Fab heavy chain
L: PC39-50I Fab light chain


Theoretical massNumber of molelcules
Total (without water)50,4402
Polymers50,4402
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-26 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.621, 131.101, 104.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody PC39-50I Fab heavy chain


Mass: 26473.635 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 PC39-50I Fab light chain


Mass: 23966.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal residue pair "VH" originates from the signal peptide
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10% glycerol, 0.1 M MES, 5% PEG 1000, 30% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17633 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 57.11 Å2 / CC1/2: 0.87 / Rpim(I) all: 0.1 / Rsym value: 0.25 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 801 / CC1/2: 0.36 / Rpim(I) all: 0.83 / Rsym value: 1.55 / % possible all: 97.6

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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: 2.7→45.81 Å / SU ML: 0.3597 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2435 884 5.02 %
Rwork0.2121 16717 -
obs0.2138 17601 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 0 4 3545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213637
X-RAY DIFFRACTIONf_angle_d0.5614950
X-RAY DIFFRACTIONf_chiral_restr0.0436547
X-RAY DIFFRACTIONf_plane_restr0.0046636
X-RAY DIFFRACTIONf_dihedral_angle_d17.87131322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.870.34781370.30862715X-RAY DIFFRACTION98.38
2.87-3.090.26361410.27752756X-RAY DIFFRACTION99.86
3.09-3.40.25371420.23032766X-RAY DIFFRACTION99.9
3.4-3.890.2561510.21852762X-RAY DIFFRACTION100
3.89-4.90.22171520.17842802X-RAY DIFFRACTION99.93
4.9-45.810.22561610.1932916X-RAY DIFFRACTION100
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)
16.2128385598-9.671580196290.6973714586562.01382377989-0.9273245788820.1008595683140.9009442953770.829624228202-0.592554114844-2.43581099686-1.108780738551.04405534681-0.0211238672151-0.64051012780.2633103727660.701561021017-0.004382417181360.04889743267340.676120187415-0.006912600588010.6568630151711.83272580779-5.26235496538-18.3713997872
22.12461155951-1.69624053802-0.8921001606276.19709905682-1.213452770672.908228415640.01443494648430.198316294448-0.336741738188-0.296581535213-0.007640171646940.5298560589160.538966884253-0.08804363503210.001789971132120.69495165851-0.00200581625305-0.125777392840.390573855783-0.04291668875160.3507944639795.28003878535-16.4274089857-11.0402540518
37.498189908023.21551775295-1.720819734642.59736804699-1.064970860282.86594675567-0.1766493787510.6256863862080.435701694362-0.3781512044450.2147781975120.10348235416-0.2692148034730.403518846323-0.01317815242730.595429435082-0.0777354944822-0.03230080040780.3706208820890.03145000060970.33323930430419.047497189115.0571373894-30.6061594002
46.128693017763.01333899363-1.739760329965.20153635519-4.001960687687.352347420730.3207435029340.3718169711580.130403440940.169294965625-0.574798723719-0.672380682221-0.1858798447530.5215868703890.2155786467530.4543400516240.122244151327-0.08486852898640.4448211238520.04305548670890.52700471980727.7610494793-10.6354267792-2.73152466336
57.735708355121.34394941322-2.387058878586.936734334771.718621434875.60666628892-0.1187378994010.59270078975-0.399400497085-0.683513286709-0.268207500152-0.395223400671.080546638920.5292451064920.3789176624020.7862470666270.18926501359-0.004357803020660.448586029284-0.05089167165280.42477842838922.8157773042-19.0848484343-11.9783825076
68.286483508440.883981473738-5.874350948866.828283645410.6453685155622.000168697630.0531476481621-0.800448911461-0.3595979753560.367887341815-0.231808139294-1.325637321021.165013057651.643238586220.1896383741640.6390677560990.241809034267-0.1150869586480.6476015616380.06929592444320.68517147190730.0580882613-18.1836863786-3.83679168488
74.045944592323.3145877427-0.5589020215645.78000219452-1.230250907420.9712342152690.0550548885111-0.0425097165272-0.254188186739-0.511383454317-0.300139081322-0.6712021226770.5356730901580.7417931465840.1962419566610.6458180420630.1857996483830.008776115554650.6370087012510.05533661326070.38482118730827.1101929015-9.09788317902-11.6644654321
85.04684277296-4.58673611528-0.3147557691099.32908271470.3006738224752.87069259213-0.2670411305490.16877865427-0.1555209382340.2595017182520.01187806537270.318060109217-0.301211665240.6995500360390.2739875344160.513109379641-0.1634408282880.08139953327150.5523471641320.084203087580.40286223186127.061133958220.089658579-21.2335026926
90.6817018611061.671579263370.823112902866.746950274290.9227487284193.230638845560.204488656299-0.4531491721330.0384155522458-0.298146540838-0.171931517972-0.971167112192-1.137131770210.747255649029-0.02014364774740.555886081551-0.22849937867-0.030496938250.6140085132620.02318274181980.56218602683825.310958638222.5193290246-12.3670421051
106.81954039643-3.091952237280.1986962084878.462864133040.165322912692.02302007121-0.212113697640.2127420341850.522653012019-0.5294811868510.0927668278146-0.544913680257-0.5077607227980.6798927034990.117588441440.571697806067-0.1749421526650.07092730333950.6338388447610.05135701839170.29314462798829.657787979421.2976256411-19.7421492288
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 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 111 )HA18 - 11118 - 137
33chain 'H' and (resid 112 through 216 )HA112 - 216138 - 242
44chain 'L' and (resid -1 through 29 )LB-1 - 291 - 32
55chain 'L' and (resid 30 through 61 )LB30 - 6133 - 64
66chain 'L' and (resid 62 through 75 )LB62 - 7565 - 78
77chain 'L' and (resid 76 through 113 )LB76 - 11379 - 117
88chain 'L' and (resid 114 through 150 )LB114 - 150118 - 154
99chain 'L' and (resid 151 through 163 )LB151 - 163155 - 167
1010chain 'L' and (resid 164 through 214 )LB164 - 214168 - 218

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