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Basic information

Entry
Database: PDB / ID: 3mme
TitleStructure and functional dissection of PG16, an antibody with broad and potent neutralization of HIV-1
Components
  • PG16 HEAVY CHAIN FAB
  • PG16 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: 3.97 Å
AuthorsPancera, M. / McLellan, J. / Zhou, T. / Zhu, J. / Kwong, P.
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
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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: PG16 HEAVY CHAIN FAB
L: PG16 LIGHT CHAIN FAB
A: PG16 HEAVY CHAIN FAB
B: PG16 LIGHT CHAIN FAB
C: PG16 HEAVY CHAIN FAB
D: PG16 LIGHT CHAIN FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0869
Polymers145,8546
Non-polymers1,2323
Water00
1
H: PG16 HEAVY CHAIN FAB
L: PG16 LIGHT CHAIN FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2053
Polymers48,6182
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-20 kcal/mol
Surface area20710 Å2
MethodPISA
2
A: PG16 HEAVY CHAIN FAB
B: PG16 LIGHT CHAIN FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8393
Polymers48,6182
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-21 kcal/mol
Surface area20840 Å2
MethodPISA
3
C: PG16 HEAVY CHAIN FAB
D: PG16 LIGHT CHAIN FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0423
Polymers48,6182
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-19 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.961, 230.804, 82.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Antibody PG16 HEAVY CHAIN FAB


Mass: 25919.049 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Production host: Homo Sapiens (human)
#2: Antibody PG16 LIGHT CHAIN FAB


Mass: 22699.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PVRC8400 / Production host: HOMO SAPIENS (human)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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

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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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 1.96M ammonium sulfate, 0.2 M NaCl, 0.1M acetate pH 4.5 with 3% 1,6 diaminohexane, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.97→50 Å / Num. obs: 5511 / % possible obs: 93.3 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.237 / Rsym value: 0.202 / Net I/σ(I): 6.9
Reflection shellResolution: 4→4.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.515 / % possible all: 82.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LRS CHAIN AB

3lrs


Resolution: 3.97→49.45 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.317 739 5.01 %
Rwork0.256 --
obs0.259 -91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 141.48 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.1622 Å20 Å2-0 Å2
2--26.54 Å2-0 Å2
3----13.3778 Å2
Refinement stepCycle: LAST / Resolution: 3.97→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9959 0 81 0 10040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310315
X-RAY DIFFRACTIONf_angle_d0.74314021
X-RAY DIFFRACTIONf_dihedral_angle_d16.8983616
X-RAY DIFFRACTIONf_chiral_restr0.0481570
X-RAY DIFFRACTIONf_plane_restr0.0031784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.973-4.27970.32541310.29412211X-RAY DIFFRACTION73
4.2797-4.71010.31751310.24882768X-RAY DIFFRACTION92
4.7101-5.39090.29641560.2332853X-RAY DIFFRACTION94
5.3909-6.78920.30611550.24722974X-RAY DIFFRACTION97
6.7892-49.45640.30851660.23423194X-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)
10.6395-1.87330.19386.52041.10722.6134-0.06730.5088-0.2187-0.5573-0.11920.0885-0.0929-0.0424-0.01090.65630.13040.20820.98570.07221.0745-2.147562.3527-20.5216
22.57760.1111-0.58782.2033-1.19931.3482-0.20620.98320.1283-0.1970.2029-0.3173-0.1524-0.27320.03670.8138-0.07740.18991.4862-0.08081.0402-28.880361.8743-6.0555
35.5688-2.1527-2.20083.0597-2.75246.54680.21640.68980.45260.23980.06060.0069-0.66440.5748-0.20890.7845-0.03290.08470.98410.15650.8707-3.294482.774-25.4077
44.3786-5.39411.95716.4845-2.62872.62720.1065-0.09480.66380.601-0.12740.03290.41110.7403-0.06271.16240.36130.04191.3716-0.2321.0482-29.235972.9435.806
51.52120.8351-1.1975.865-1.11640.89520.75010.1734-0.40450.0409-0.3201-0.57080.001-0.0753-0.17350.91140.0979-0.10651.0430.18381.4871-14.994717.492310.1392
62.6555-0.22771.43434.6554-2.29391.7792-0.09730.00550.21580.3464-0.28910.0115-0.15970.74480.63420.78440.1980.0240.9993-0.03070.862-44.256715.2818-0.8495
75.3021-0.81221.95916.58540.01222.13180.0731-0.2338-0.3120.32880.2426-0.2441-0.50720.5363-0.37570.5226-0.07950.13540.62180.19480.8201-14.706238.39068.3446
83.613-1.52170.64784.1798-3.9837.0924-0.6001-0.6987-0.1137-0.0581-0.03950.46521.04430.60820.32460.79350.4002-0.0010.9325-0.13280.8364-53.979423.67389.2785
92.5085-0.2915-0.52050.43460.56870.708-0.06790.2356-0.6448-0.38090.3869-0.20510.18550.06280.34522.15870.4620.81811.55940.16591.6684-24.027918.2761-35.559
102.46151.758-0.29921.8763-0.09930.0451-0.86690.56110.5475-1.5103-1.1831-0.8191-0.6401-0.9311.36073.02290.78150.361.65260.37351.128-27.218948.8217-36.8513
114.2362-1.3081-1.01863.489-2.99563.65450.55930.08420.0078-1.0270.00060.39930.1093-1.0005-0.23272.20580.52560.17331.37630.07091.2463-45.618418.4651-31.8152
125.42480.22211.28261.06811.51713.9192-2.2571-0.25990.5605-0.77321.0365-0.57241.21051.88951.29372.71740.44090.08861.03710.01670.6672-37.737252.6925-48.6991
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 138:238
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 138:238
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 138:238

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