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- PDB-3lrs: Structure of PG16, an antibody with broad and potent neutralizati... -

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Basic information

Entry
Database: PDB / ID: 3lrs
TitleStructure of PG16, an antibody with broad and potent neutralization of HIV-1
Components
  • PG-16 Heavy Chain Fab
  • PG-16 Light Chain Fab
KeywordsIMMUNE SYSTEM / neutralizing antibodies / long CDRH3 / HIV-1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsPancera, M. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2010
Title: Crystal structure of PG16 and chimeric dissection with somatically related PG9: structure-function analysis of two quaternary-specific antibodies that effectively neutralize HIV-1.
Authors: Pancera, M. / McLellan, J.S. / Wu, X. / Zhu, J. / Changela, A. / Schmidt, S.D. / Yang, Y. / Zhou, T. / Phogat, S. / Mascola, J.R. / Kwong, P.D.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PG-16 Heavy Chain Fab
L: PG-16 Light Chain Fab
A: PG-16 Heavy Chain Fab
B: PG-16 Light Chain Fab
C: PG-16 Heavy Chain Fab
D: PG-16 Light Chain Fab
E: PG-16 Heavy Chain Fab
F: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,21912
Polymers192,3348
Non-polymers8854
Water7,008389
1
H: PG-16 Heavy Chain Fab
L: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-21 kcal/mol
Surface area18970 Å2
MethodPISA
2
A: PG-16 Heavy Chain Fab
B: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-21 kcal/mol
Surface area19300 Å2
MethodPISA
3
C: PG-16 Heavy Chain Fab
D: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-20 kcal/mol
Surface area19500 Å2
MethodPISA
4
E: PG-16 Heavy Chain Fab
F: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-20 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.317, 165.085, 81.363
Angle α, β, γ (deg.)90.00, 91.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
PG-16 Heavy Chain Fab


Mass: 25919.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#2: Antibody
PG-16 Light Chain Fab


Mass: 22164.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Organ (production host): KIDNEY / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / pH: 10.5
Details: 0.74M Potassium Dihydrogen Phosphate, 1.10M Sodium Dihydrogen Phosphate, 0.2M Lithium Sulfate Monohydrate, 0.1 M CAPS, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 71375 / % possible obs: 81.5 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Rsym value: 0.099 / Net I/σ(I): 15.73
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5116 / Mean I/σ(I) obs: 1.49 / Rsym value: 0.514 / % possible all: 25.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NLO

1nlo


Resolution: 2.37→30.59 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 3598 5.04 %
Rwork0.211 --
obs0.213 71375 82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.03 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 65.38 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å2-0 Å2-8.961 Å2
2---2.786 Å2-0 Å2
3----0.364 Å2
Refinement stepCycle: LAST / Resolution: 2.37→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12979 0 56 389 13424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813375
X-RAY DIFFRACTIONf_angle_d1.15418170
X-RAY DIFFRACTIONf_dihedral_angle_d16.0984677
X-RAY DIFFRACTIONf_chiral_restr0.0682041
X-RAY DIFFRACTIONf_plane_restr0.0052317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.3990.427410.265902X-RAY DIFFRACTION28
2.399-2.4320.358580.261252X-RAY DIFFRACTION40
2.432-2.4660.327900.261384X-RAY DIFFRACTION43
2.466-2.5030.352810.2761522X-RAY DIFFRACTION49
2.503-2.5420.332960.2751750X-RAY DIFFRACTION54
2.542-2.5840.3631060.2641857X-RAY DIFFRACTION60
2.584-2.6280.3311250.2612081X-RAY DIFFRACTION65
2.628-2.6760.2951020.2792197X-RAY DIFFRACTION71
2.676-2.7280.3511270.2742424X-RAY DIFFRACTION75
2.728-2.7830.3431360.2722520X-RAY DIFFRACTION80
2.783-2.8440.3481360.2572716X-RAY DIFFRACTION86
2.844-2.910.2871440.2582956X-RAY DIFFRACTION91
2.91-2.9830.3131450.2483023X-RAY DIFFRACTION96
2.983-3.0630.3061600.2483103X-RAY DIFFRACTION98
3.063-3.1530.3131700.2353152X-RAY DIFFRACTION99
3.153-3.2550.2841700.2283172X-RAY DIFFRACTION100
3.255-3.3710.2661640.2143153X-RAY DIFFRACTION100
3.371-3.5060.2991750.2033162X-RAY DIFFRACTION100
3.506-3.6650.2611830.1863154X-RAY DIFFRACTION99
3.665-3.8580.2211400.193197X-RAY DIFFRACTION100
3.858-4.0990.2371810.1663159X-RAY DIFFRACTION100
4.099-4.4150.1851710.1443146X-RAY DIFFRACTION100
4.415-4.8580.1931840.143198X-RAY DIFFRACTION100
4.858-5.5570.2051770.1583186X-RAY DIFFRACTION100
5.557-6.9880.31590.2043205X-RAY DIFFRACTION100
6.988-30.5930.2211770.2213206X-RAY DIFFRACTION99
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)
12.7617-0.4191.65830.6889-0.10981.5554-0.14770.06590.2459-0.40850.1581-0.024-0.3473-0.130.00590.51890.0654-0.04320.2612-0.02730.2405-20.9146-11.5481-24.6659
22.0461.12570.11723.49630.440.20690.3788-0.7203-0.121.1481-0.45430.1546-0.0507-0.07870.01750.6956-0.10060.09880.4611-0.0840.1189-33.0956-38.8584-24.4563
33.7274-0.04661.56821.98350.13993.03280.35860.10350.1089-0.0951-0.1239-0.22280.250.1679-0.21860.4452-0.0128-0.02920.2816-0.0390.3487-3.1257-21.1064-17.3239
45.10432.0483-1.98891.2039-1.1931.19760.5426-0.7636-0.23080.5414-0.3843-0.1539-0.26040.3-0.07070.5139-0.011-0.17820.3887-0.08470.2356-24.4448-49.6801-33.4941
51.28960.1322.05911.38580.73553.25470.17430.1099-0.1064-0.11330.00440.43490.3116-0.021-0.12810.29640.0302-0.04080.2723-0.04760.410417.6751-66.0202-62.2785
60.73170.72551.05772.9911-0.80872.10620.14360.3050.1930.0402-0.3974-0.6813-0.03760.81320.30380.18550.04360.10080.53840.04270.724618.2682-38.7141-74.4006
72.70540.0011.6212.54550.44192.9454-0.3247-0.2040.17510.42970.04030.0130.1946-0.15670.23430.42520.03920.01260.36440.00910.289424.501-56.4714-44.269
82.23481.0227-0.98641.4991-2.70284.37040.0793-0.2355-0.41750.184-0.3903-0.4905-0.05020.62140.26290.34260.0994-0.18090.4120.01810.47249.0307-27.9312-66.225
92.889-0.0396-1.7880.44790.75331.4078-0.1468-0.0593-0.081-0.03010.33440.04810.1901-0.0706-0.08660.45070.0751-0.04980.297-0.00690.2663-17.9234-24.6881-65.3901
101.1492-0.6758-0.07765.1109-0.54440.0826-0.0854-0.14690.19260.6650.0729-0.0697-0.3550.3331-0.05080.7532-0.0291-0.08830.3397-0.04560.2585-3.21952.3814-64.8765
111.98241.8518-2.10243.2965-1.37034.680.23840.19580.1420.02810.09460.4562-0.3673-0.3069-0.31990.3331-0.0107-0.01060.30270.03650.3191-35.5592-14.8063-58.539
124.87732.7920.60271.2808-0.03772.9610.4444-0.33330.45240.3978-0.0250.3630.1258-0.4397-0.33560.4738-0.00480.15230.35550.13660.3273-11.181413.4095-73.6186
132.1745-0.7393-2.04010.01120.17022.3995-0.21-0.13430.1257-0.01520.246-0.1214-0.0840.0343-0.03830.277-0.0098-0.05160.2936-0.06920.3262-23.1132-52.8585-60.345
140.9704-0.2008-0.28914.61520.89721.30240.0132-0.08-0.11510.1941-0.0622-0.73990.18260.09080.06360.26110.0254-0.09710.3010.03640.5835-22.961-79.9321-45.5817
154.65111.0445-2.02352.7707-1.42851.1971-0.36530.3277-0.3638-0.54240.189-0.05550.0666-0.2740.17830.4666-0.0571-0.00790.3324-0.01360.2825-15.7998-62.7513-77.7682
165.99841.8823-0.51271.5785-2.67184.7961-0.48830.5025-0.0357-0.3414-0.0183-0.1140.63320.28490.4490.4252-0.1190.15570.35190.03560.3246-31.3674-91.149-54.8834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN L AND RESID 1:112
2X-RAY DIFFRACTION2CHAIN L AND RESID 113:213
3X-RAY DIFFRACTION3CHAIN H AND RESID 1:137
4X-RAY DIFFRACTION4CHAIN H AND RESID 138:239
5X-RAY DIFFRACTION5CHAIN B AND RESID 1:112
6X-RAY DIFFRACTION6CHAIN B AND RESID 113:213
7X-RAY DIFFRACTION7CHAIN A AND RESID 1:137
8X-RAY DIFFRACTION8CHAIN A AND RESID 138:239
9X-RAY DIFFRACTION9CHAIN D AND RESID 1:112
10X-RAY DIFFRACTION10CHAIN D AND RESID 113:213
11X-RAY DIFFRACTION11CHAIN C AND RESID 1:137
12X-RAY DIFFRACTION12CHAIN C AND RESID 138:239
13X-RAY DIFFRACTION13CHAIN F AND RESID 1:112
14X-RAY DIFFRACTION14CHAIN F AND RESID 113:213
15X-RAY DIFFRACTION15CHAIN E AND RESID 1:137
16X-RAY DIFFRACTION16CHAIN E AND RESID 138:239

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