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- PDB-6b3d: Crystal structure of anti-HIV antibody PGT128 in complex with a b... -

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Basic information

Entry
Database: PDB / ID: 6b3d
TitleCrystal structure of anti-HIV antibody PGT128 in complex with a bacterially derived synthetic mimetic of Man9.
Components
  • PGT128 Fab heavy chain
  • PGT128 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / glycan / mannose
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ISOPROPYL ALCOHOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 Å
AuthorsMurrell, S. / Wilson, I.A.
CitationJournal: Nat Commun / Year: 2017
Title: Bacterially derived synthetic mimetics of mammalian oligomannose prime antibody responses that neutralize HIV infectivity.
Authors: Pantophlet, R. / Trattnig, N. / Murrell, S. / Lu, N. / Chau, D. / Rempel, C. / Wilson, I.A. / Kosma, P.
History
DepositionSep 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PGT128 Fab light chain
H: PGT128 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,00716
Polymers47,7862
Non-polymers2,22014
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint37 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.137, 105.204, 145.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody PGT128 Fab light chain


Mass: 22223.588 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 PGT128 Fab heavy chain


Mass: 25562.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a1122h-1a_1-5]/1-1-1-1-1-1-1/a3-b1_a6-e1_b2-c1_c2-d1_e6-f1_f2-g1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 165 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.085 M HEPES pH 7.5, 8.5% isopropanol, 10% ethylene glycol, 15% glycerol, and 17% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 25900 / % possible obs: 99.8 % / Redundancy: 11.8 % / CC1/2: 0.99 / Rpim(I) all: 0.029 / Rsym value: 0.102 / Net I/σ(I): 22.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TV3

3tv3


Resolution: 2.271→36.326 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 1277 4.95 %
Rwork0.163 --
obs0.1648 25806 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.271→36.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 147 152 3605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033566
X-RAY DIFFRACTIONf_angle_d0.6674880
X-RAY DIFFRACTIONf_dihedral_angle_d14.5492132
X-RAY DIFFRACTIONf_chiral_restr0.044571
X-RAY DIFFRACTIONf_plane_restr0.004597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2713-2.36230.21421300.17442627X-RAY DIFFRACTION98
2.3623-2.46970.23131330.18512692X-RAY DIFFRACTION100
2.4697-2.59990.26081450.19382688X-RAY DIFFRACTION100
2.5999-2.76280.2471390.19542733X-RAY DIFFRACTION100
2.7628-2.9760.2341210.1822706X-RAY DIFFRACTION100
2.976-3.27530.20671420.17542735X-RAY DIFFRACTION100
3.2753-3.74880.19931530.15982742X-RAY DIFFRACTION100
3.7488-4.72150.15781460.13362742X-RAY DIFFRACTION100
4.7215-36.33110.17951680.15372864X-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)
12.1398-0.03412.00290.62860.17221.61340.0773-0.5478-0.11980.1811-0.0410.11460.2581-0.3841-0.05490.2654-0.04040.00760.32630.00180.198-29.6227-2.176519.9805
22.68390.72892.23951.14140.09852.5857-0.1168-0.57720.16210.0762-0.07480.1009-0.1468-0.68170.19590.301-0.0030.02460.4105-0.08990.2264-33.80834.831422.4946
31.3432-0.86071.93882.101-0.71853.24520.1657-0.2641-0.1214-0.08790.0518-0.0358-0.0742-0.0485-0.10170.188-0.0504-0.0070.27140.01980.1961-28.5509-0.712116.2239
41.04370.04681.41170.3576-0.02892.27340.3261-0.3694-0.28480.1703-0.06430.05690.12990.2238-0.29280.3493-0.0917-0.05150.43210.04350.1982-25.4034-5.57523.6947
52.1782-1.24640.54233.18550.17680.75210.1139-0.0205-0.1208-0.06220.0804-0.17630.20680.176-0.15580.2420.0354-0.02570.2352-0.00430.272-17.8837-27.83152.8759
61.8013-2.71611.28784.2556-1.67672.39950.1053-0.18610.0404-0.0425-0.043-0.13820.22160.1287-0.09290.2073-0.0172-0.01440.22710.01740.2286-26.5045-20.76597.6886
72.1814-0.1088-0.29682.69870.09882.04440.0746-0.12320.02410.11880.0387-0.08240.0277-0.0108-0.15380.24740.043-0.01230.2425-0.00330.2838-21.4879-20.34977.4476
81.9977-1.09440.49341.7140.51651.1555-0.1392-0.3669-0.58220.16750.5054-0.15470.55620.1196-0.1540.46130.1013-0.05980.24690.04430.4536-14.303-34.250811.0046
93.3165-2.91631.0587.7296-1.0311.79320.0946-0.041-0.67890.4341-0.13780.08230.2524-0.0736-0.02110.299-0.02390.01020.24150.0310.4414-26.4435-32.05287.6958
102.14310.1983-0.38762.50431.90232.52750.31590.4019-0.31280.0992-0.1651-0.49820.26140.3163-0.15310.31320.0314-0.12080.3211-0.07770.3565-2.0693-3.841621.3233
112.64920.57991.13121.0166-0.17552.0980.23-0.3285-0.15550.3311-0.1308-0.17010.1811-0.2365-0.07770.312-0.0318-0.0960.26210.00790.2267-8.973-0.054431.9944
122.4210.34290.35661.07210.41333.8760.1015-0.65030.17390.3344-0.07760.0924-0.0651-0.43610.05970.2882-0.0253-0.04580.4606-0.03540.2186-18.1624.122134.0914
131.9145-1.9256-1.22183.50942.16871.88680.05510.0082-0.00350.27480.1339-0.51480.08950.0482-0.17160.27760.0448-0.10860.3047-0.04870.3188-7.5293-6.724517.6812
143.1018-1.57710.62432.7988-0.89151.78910.19330.0396-0.5092-0.26440.16660.06840.1076-0.4842-0.22250.2886-0.0146-0.05380.4020.01010.3447-15.0984-31.007-4.8272
151.6975-0.03981.02371.79550.30242.4565-0.0542-0.1150.04710.21730.1944-0.4711-0.0354-0.0093-0.1040.19740.0285-0.02080.1898-0.03090.3492-7.5338-21.0174-1.5695
161.6434-0.24470.31962.21310.72221.54130.1025-0.19540.07620.14710.1297-0.30510.1622-0.2635-0.16440.19720.0003-0.01030.2123-0.00230.2861-12.6838-21.0386-0.996
173.41490.08231.84772.20281.3043.33920.00640.2363-0.2036-0.02140.2043-0.50010.0970.2341-0.17730.224-0.00210.04410.224-0.03370.3927-5.0752-25.6569-7.807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 3 through 49 )
2X-RAY DIFFRACTION2chain 'L' and (resid 50 through 75 )
3X-RAY DIFFRACTION3chain 'L' and (resid 76 through 92 )
4X-RAY DIFFRACTION4chain 'L' and (resid 93 through 106A)
5X-RAY DIFFRACTION5chain 'L' and (resid 107 through 137 )
6X-RAY DIFFRACTION6chain 'L' and (resid 138 through 150 )
7X-RAY DIFFRACTION7chain 'L' and (resid 151 through 173 )
8X-RAY DIFFRACTION8chain 'L' and (resid 174 through 187 )
9X-RAY DIFFRACTION9chain 'L' and (resid 188 through 210 )
10X-RAY DIFFRACTION10chain 'H' and (resid 2 through 17 )
11X-RAY DIFFRACTION11chain 'H' and (resid 18 through 87 )
12X-RAY DIFFRACTION12chain 'H' and (resid 88 through 100I)
13X-RAY DIFFRACTION13chain 'H' and (resid 100J through 119 )
14X-RAY DIFFRACTION14chain 'H' and (resid 120 through 134 )
15X-RAY DIFFRACTION15chain 'H' and (resid 135 through 157 )
16X-RAY DIFFRACTION16chain 'H' and (resid 158 through 188 )
17X-RAY DIFFRACTION17chain 'H' and (resid 189 through 215 )

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