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- PDB-3mug: Crystal structure of human Fab PG16, a broadly reactive and poten... -

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Basic information

Entry
Database: PDB / ID: 3mug
TitleCrystal structure of human Fab PG16, a broadly reactive and potent HIV-1 neutralizing antibody
Components
  • Antibody PG16 Heavy Chain
  • Antibody PG16 Light Chain
KeywordsIMMUNE SYSTEM / PG16 / Fab / sulfotyrosine / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsPejchal, R. / Walker, L.M. / Burton, D.R. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1.
Authors: Pejchal, R. / Walker, L.M. / Stanfield, R.L. / Phogat, S.K. / Koff, W.C. / Poignard, P. / Burton, D.R. / Wilson, I.A.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 3.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody PG16 Light Chain
B: Antibody PG16 Heavy Chain
C: Antibody PG16 Light Chain
D: Antibody PG16 Heavy Chain
E: Antibody PG16 Light Chain
F: Antibody PG16 Heavy Chain
G: Antibody PG16 Light Chain
H: Antibody PG16 Heavy Chain
I: Antibody PG16 Light Chain
J: Antibody PG16 Heavy Chain
K: Antibody PG16 Light Chain
L: Antibody PG16 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,88615
Polymers293,81612
Non-polymers1,0703
Water7,764431
1
A: Antibody PG16 Light Chain
B: Antibody PG16 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1913
Polymers48,9692
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-18 kcal/mol
Surface area20410 Å2
MethodPISA
2
C: Antibody PG16 Light Chain
D: Antibody PG16 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3943
Polymers48,9692
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-16 kcal/mol
Surface area20860 Å2
MethodPISA
3
G: Antibody PG16 Light Chain
H: Antibody PG16 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)48,9692
Polymers48,9692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-22 kcal/mol
Surface area20300 Å2
MethodPISA
4
I: Antibody PG16 Light Chain
J: Antibody PG16 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3943
Polymers48,9692
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-17 kcal/mol
Surface area20830 Å2
MethodPISA
5
K: Antibody PG16 Light Chain
L: Antibody PG16 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)48,9692
Polymers48,9692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-22 kcal/mol
Surface area20360 Å2
MethodPISA
6
E: Antibody PG16 Light Chain
F: Antibody PG16 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)48,9692
Polymers48,9692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.770, 66.250, 198.700
Angle α, β, γ (deg.)90.00, 98.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Antibody PG16 Light Chain


Mass: 22682.018 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293S GnTI -/- / Production host: Homo sapiens (human)
#2: Antibody
Antibody PG16 Heavy Chain


Mass: 26287.389 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293S GnTI -/- / Production host: Homo sapiens (human)
#3: 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.: 2
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
#4: 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.: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 40% PEG 400, 0.08M sodium chloride, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.49→24.97 Å / Num. all: 116950 / Num. obs: 110752 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 54.99 Å2 / Rsym value: 0.097 / Net I/σ(I): 7.5
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 14574 / Rsym value: 0.507 / % possible all: 85.9

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7FAB

7fab


Resolution: 2.49→24.97 Å / Cor.coef. Fo:Fc: 0.9423 / Cor.coef. Fo:Fc free: 0.9178 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 5547 5.01 %RANDOM
Rwork0.2074 ---
obs0.2094 110627 94.7 %-
Displacement parametersBiso mean: 60.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.097 Å20 Å2-4.1292 Å2
2--0.8589 Å20 Å2
3---1.2381 Å2
Refine analyzeLuzzati coordinate error obs: 0.414 Å
Refinement stepCycle: LAST / Resolution: 2.49→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20129 0 70 431 20630
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01207552
X-RAY DIFFRACTIONt_angle_deg1.25283362
X-RAY DIFFRACTIONt_dihedral_angle_d65582
X-RAY DIFFRACTIONt_trig_c_planes3872
X-RAY DIFFRACTIONt_gen_planes31075
X-RAY DIFFRACTIONt_it2075520
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion20.47
X-RAY DIFFRACTIONt_chiral_improper_torsion27485
X-RAY DIFFRACTIONt_ideal_dist_contact215244
LS refinement shellResolution: 2.49→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2647 377 5.1 %
Rwork0.2143 7008 -
all0.2169 7385 -
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)
10.53060.70320.45683.868-1.25080.8685-0.01360.4041-0.0735-0.27640.30490.5682-0.0316-0.2664-0.2913-0.20380.08750.0028-0.0740.07130.04812.4375-5.47678.2172
20.23320.34870.0487.4128-3.09361.25690.06260.1217-0.46250.2331-0.1627-0.39130.2690.11920.1001-0.17150.0103-0.0069-0.0202-0.0513-0.086617.0404-8.082585.1011
31.229-0.0697-0.25471.13060.30064.4062-0.23240.3612-0.2559-0.71330.3301-0.5792-0.5113-0.026-0.09770.0319-0.15430.1126-0.1724-0.0308-0.1515-8.787722.552351.3891
41.3227-0.7280.81340.9276-0.9856.3038-0.04790.26080.1161-0.49780.1286-0.1197-0.8096-0.3838-0.08070.035-0.073-0.0171-0.2112-0.0027-0.3069-23.99828.946448.9179
50.5989-0.5405-0.85120.61480.40621.681-0.1721-0.0236-0.2012-0.2668-0.01840.1053-0.0925-0.22860.19050.5672-0.0329-0.0311-0.3054-0.0301-0.297121.37426.960215.4766
61.6826-0.6894-1.69090.99930.19493.8018-0.3322-0.2024-0.12860.16380.12890.17390.3686-0.06620.20320.6695-0.09570.0504-0.461-0.0275-0.359722.1935-6.806521.2707
70.66080.40910.06083.4988-1.19071.123200.3312-0.0879-0.0260.23150.2976-0.0418-0.316-0.2315-0.12910.1126-0.01-0.07960.0269-0.124266.94-5.464678.8636
80.1291-0.35660.35186.7982-2.87831.25030.07920.0982-0.30780.1983-0.2758-0.38380.22030.18690.1966-0.10920.0420.0015-0.0732-0.0446-0.121681.6913-8.040585.3118
90.9476-0.0394-0.63551.2303-0.98373.6616-0.04340.0748-0.037-0.2825-0.0164-0.1212-0.0169-0.18310.0598-0.0772-0.0041-0.0101-0.21440.0203-0.183656.284722.412752.0197
100.9164-0.46350.67570.9105-1.55965.3464-0.01880.05330.2963-0.35360.0438-0.0093-0.3388-0.5472-0.025-0.00290.02390.0156-0.189-0.0607-0.243741.709228.745349.0009
110.7679-0.4726-1.45370.67610.01351.5902-0.08240.0036-0.1539-0.1454-0.05430.05370.0608-0.16650.13660.4866-0.0348-0.0129-0.2903-0.0164-0.283583.54596.981515.8096
121.5686-0.5026-1.97410.41560.38583.0297-0.1818-0.063-0.1179-0.01940.01920.11550.2901-0.00280.16260.5837-0.0210.0318-0.39360.0273-0.30884.6857-6.802321.7007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 213
2X-RAY DIFFRACTION1A505
3X-RAY DIFFRACTION2B1 - 239
4X-RAY DIFFRACTION3C2 - 213
5X-RAY DIFFRACTION3C505 - 506
6X-RAY DIFFRACTION4D1 - 239
7X-RAY DIFFRACTION5E3 - 213
8X-RAY DIFFRACTION6F1 - 238
9X-RAY DIFFRACTION7G2 - 213
10X-RAY DIFFRACTION8H1 - 239
11X-RAY DIFFRACTION9I2 - 213
12X-RAY DIFFRACTION9I505 - 506
13X-RAY DIFFRACTION10J1 - 239
14X-RAY DIFFRACTION11K3 - 213
15X-RAY DIFFRACTION12L1 - 238

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