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- PDB-8gc1: Crystal structure of the unmutated common ancestor (UCA) of the P... -

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Basic information

Entry
Database: PDB / ID: 8gc1
TitleCrystal structure of the unmutated common ancestor (UCA) of the PC39-1 anti-HIV broadly neutralizing antibody lineage
Components
  • PC39-1 UCA Fab heavy chain
  • PC39-1 UCA 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: 3.19 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 1.2Nov 20, 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: PC39-1 UCA Fab heavy chain
L: PC39-1 UCA Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,2212
Polymers48,2212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-21 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.503, 156.114, 77.024
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 PC39-1 UCA Fab heavy chain


Mass: 24685.578 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 PC39-1 UCA Fab light chain


Mass: 23535.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.72 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 10.5 / Details: 0.2 M sodium chloride, 0.1 M CAPS, 20% PEG 8000

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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: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 12341 / % possible obs: 98.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 75.25 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.09 / Rsym value: 0.16 / Net I/σ(I): 6
Reflection shellResolution: 3.19→3.38 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2179 / CC1/2: 0.69 / Rpim(I) all: 0.7 / Rsym value: 0.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→47.71 Å / SU ML: 0.4744 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.451
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2983 634 5.16 %
Rwork0.2705 11656 -
obs0.2719 12290 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.37 Å2
Refinement stepCycle: LAST / Resolution: 3.19→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 0 3211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183287
X-RAY DIFFRACTIONf_angle_d0.51234475
X-RAY DIFFRACTIONf_chiral_restr0.0419505
X-RAY DIFFRACTIONf_plane_restr0.0045571
X-RAY DIFFRACTIONf_dihedral_angle_d9.99561176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.440.42481250.37682259X-RAY DIFFRACTION98.59
3.44-3.780.39731170.31992313X-RAY DIFFRACTION99.14
3.78-4.330.31021340.26582304X-RAY DIFFRACTION99.88
4.33-5.450.22331290.21752342X-RAY DIFFRACTION99.72
5.45-47.710.27661290.26092438X-RAY DIFFRACTION99.53
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)
15.615097635370.286881255501-0.5207902960525.72628806266-2.076273274482.13346519194-0.1224228503220.007310250470770.4023259129980.468605572136-0.03629115789610.297867659519-1.22181974737-0.488025101447-0.009778907834821.386906876080.1362286904520.03270445208910.612466129490.008670223877160.496292660336-35.11595782592.1452139966724.2249828751
23.472922760442.52679659315-1.923196707374.09174744868-0.8472991746142.172220918180.0966504740633-0.28306491260.4436933969890.3387170949750.3345183441030.655803516739-0.83363633114-0.432290307396-0.3140172341910.9692344368110.1324472678820.1412922254050.568712048475-0.003634639674410.510250242629-36.06244333410.92331267050624.3412763285
30.8877718512990.607224365293-0.0526923939573.41412023677-0.3216299946854.41985393584-0.6848378435130.230662065523-1.316216714821.06088241877-0.04541670649980.6890733026881.18947574013-0.4158824537970.2398360250651.2294731369-0.2734690856690.09401230722420.5882699572490.03294938743790.62596382532-30.7333779185-31.488830656319.7146353692
48.05073137736-2.34780494662-0.1525140249462.504534302630.8001596050763.06276741498-0.439156517678-0.543619938844-0.5781468159690.9441967190320.3372784779770.1455447131580.8137327310990.02237800992250.1160114244391.47334566659-0.149616144199-0.03269956272750.4739455131820.08614197018390.605815374601-23.9836933628-31.97920769823.5058625758
52.17259828991-3.063910088411.718082572534.67779783373-2.826830268836.54082087985-0.5140657581140.184352527264-0.04937186435090.9253698198640.127498092299-0.0643525611578-0.06349374518880.3064510515990.3071762998791.14271511548-0.08776162205850.04200640058750.382448810520.00722027963280.752889873963-15.0413462513-1.96989518966.08743421594
62.64169944128-0.305688160521-0.537272570312.594708727081.510492941724.49744526258-0.188155866452-0.1393613745630.1935041300741.184890355710.03335137808180.198936981169-1.373712705960.7184616343750.1294073151941.32325002671-0.177813923277-0.06540871187750.5504217227330.05818879102070.633450523945-16.22348317295.748680127212.9908969689
71.860939147081.471999101250.01678238293.90418933180.004286262927962.881613014110.233674066384-0.2031309659-0.1014368367160.511219457361-0.421857909505-0.249235688109-0.082472257979-0.1377172535150.1328905011681.402600190180.00819852676078-0.0651833124330.577985488360.05901916944040.48642603332-19.8865620267-16.511150399611.6682273253
85.450060704742.256806926830.2211597436474.095450883881.169553275363.5862861139-0.7010045855360.5009799622160.45871754031-1.252247588890.110028029866-0.0109481336556-0.1138053663170.209903635750.6193239429911.07536584149-0.0318736593305-0.05953976622190.4657957309920.061609961290.594852047232-21.2902947121-25.93541304055.42813614733
96.022714417695.594677477811.219426849997.482813011031.241550826670.187850470852-0.3223719542640.1832883060980.289104735495-0.8019222729020.054537970570.360383050887-0.05267427357320.02135880725790.4443630149971.45133010172-0.108458220709-0.06016975529610.544727060340.04876460054680.572547137945-24.8016476567-36.43903346362.99219656871
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 - 63
22chain 'H' and (resid 64 through 109 )HA64 - 10964 - 110
33chain 'H' and (resid 110 through 145 )HA110 - 145111 - 139
44chain 'H' and (resid 146 through 214 )HA146 - 214140 - 208
55chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
66chain 'L' and (resid 19 through 75 )LB19 - 7519 - 76
77chain 'L' and (resid 76 through 139 )LB76 - 13977 - 141
88chain 'L' and (resid 140 through 172 )LB140 - 172142 - 174
99chain 'L' and (resid 173 through 213 )LB173 - 213175 - 215

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