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- PDB-7rdm: Crystal structure of PCDN-38B, a broadly neutralizing anti-HIV an... -

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Basic information

Entry
Database: PDB / ID: 7rdm
TitleCrystal structure of PCDN-38B, a broadly neutralizing anti-HIV antibody
Components(PCDN-38B Fab ...) x 2
KeywordsIMMUNE SYSTEM / Antibody / Broadly Neutralizing / HIV-1 / Cysteinylation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CYSTEINE / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsOmorodion, 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: J.Mol.Biol. / Year: 2021
Title: Structural and Biochemical Characterization of Cysteinylation in Broadly Neutralizing Antibodies to HIV-1.
Authors: Omorodion, O. / Wilson, I.A.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PCDN-38B Fab light chain
B: PCDN-38B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,99317
Polymers48,6422
Non-polymers2,35115
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-31 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.696, 68.065, 77.937
Angle α, β, γ (deg.)90.000, 96.646, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody PCDN-38B Fab light chain


Mass: 23399.936 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 PCDN-38B Fab heavy chain


Mass: 25242.303 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 , 2 types, 2 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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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Non-polymers , 4 types, 272 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.6 M sodium dihydrogen phosphate, 0.4 M dipotassium hydrogen phosphate, 0.1 M phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03309 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03309 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 36353 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.55 Å2 / CC1/2: 1 / Rsym value: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 2.08→2.2 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5694 / CC1/2: 0.7 / Rsym value: 0.98 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BZD

5bzd


Resolution: 2.08→45.5 Å / SU ML: 0.2876 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1878 5.17 %
Rwork0.1908 34426 -
obs0.1923 36304 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.61 Å2
Refinement stepCycle: LAST / Resolution: 2.08→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 150 259 3824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253690
X-RAY DIFFRACTIONf_angle_d0.57815027
X-RAY DIFFRACTIONf_chiral_restr0.0449582
X-RAY DIFFRACTIONf_plane_restr0.0047626
X-RAY DIFFRACTIONf_dihedral_angle_d18.20591346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.33971380.30112503X-RAY DIFFRACTION94.46
2.14-2.20.3431520.29362628X-RAY DIFFRACTION99.18
2.2-2.270.33151560.27892623X-RAY DIFFRACTION99.11
2.27-2.350.30171440.25942643X-RAY DIFFRACTION99.25
2.35-2.440.29781270.25132659X-RAY DIFFRACTION99.54
2.44-2.560.27371060.22792662X-RAY DIFFRACTION99.46
2.56-2.690.28691390.22752668X-RAY DIFFRACTION99.54
2.69-2.860.22611530.21612642X-RAY DIFFRACTION99.32
2.86-3.080.26721690.20812661X-RAY DIFFRACTION99.89
3.08-3.390.20171410.18212673X-RAY DIFFRACTION99.82
3.39-3.880.15931430.1562652X-RAY DIFFRACTION99.75
3.88-4.890.17481350.13342716X-RAY DIFFRACTION99.62
4.89-45.50.18361750.17592696X-RAY DIFFRACTION99.31
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)
13.16465387167-1.472223348992.406707227721.9694262156-0.635558908466.282347352160.33465865034-0.198470630546-0.5561246120270.1214933894330.2343254175780.2628262525120.804211027908-0.464202668962-0.504175325730.335878367183-0.117956084456-0.01326695221950.3655111962310.06904035646570.4189994842946.724-1.62829.007
24.57769659196-0.9873189294960.8871656999983.913034481331.123866746223.197397218320.105999093337-0.376884924042-0.07576036019460.2761879044140.1829957647910.396689421788-0.0773447021467-0.854980374999-0.3057313575050.420123250257-0.02356270316480.04896220775250.5821367211370.02771607213040.3515443984494.9687.12734.546
30.03019486358710.1796973480170.07266010264330.915451860678-0.2028325697363.271635936410.0592901294991-0.113716506081-0.02955278138820.119593863384-0.02772575378970.01550624183340.0577074120045-0.0810578033926-0.04562714969940.3043198613950.01557342501020.007087672230110.266484186991-0.002663552226450.32186832295313.0888.41615.478
45.63313843054-1.89293573431-3.73678719320.9152008120360.6283612020924.4409261367-0.0424157419302-0.159130775077-0.183012125666-0.118493722047-0.07629929386870.0938796263920.172954771030.154032061090.1698390049050.3419611473930.0171593468539-0.008171207713470.2799999505050.01205806947670.31990428072519.9523.558-0.437
55.577234534010.0142344107739-3.916755441291.19552893306-0.3576875738986.22427963947-0.0559311648362-0.0659216821482-0.080164836978-0.2475383602120.00615010804945-0.0918262719825-0.02312828024480.39035573610.07247053477790.3210839659170.03670430398770.0005755238596470.200596780061-0.0170444643730.30620580059819.9557.279-3.997
63.30699081859-1.897830328720.399131320162.907883384540.3151850242993.19805559705-0.01655160778440.05742808006070.2674262387650.229856218995-0.12594191629-0.156108568384-0.3470945230580.2437100499980.1426093606830.430684395963-0.0531373022204-0.01638068937760.4201934183830.043391287770.32294403138625.19815.30137.625
70.109700229402-0.263969863745-0.2628328453740.3359268032750.01494583506144.25507269109-0.02398048563390.03796039105070.1036950662920.11857388258-0.0489879050962-0.113213709779-0.1661841284780.2009034173390.05299657136440.400347039966-0.0335793924974-0.02880114448960.4516768800930.01887065144730.37240568822724.74413.38738.761
82.89580824598-0.21020874639-4.184454911989.047448596430.8020448547176.072672460940.05978446934081.230398667840.0032641634419-0.9666505690480.06184613748920.667363261254-0.215332885865-0.774355514914-0.2627046738170.3675218013340.01212827875760.01298632005730.4177161243280.006777160862310.30278331190920.88419.665-5.651
92.10878104233-0.2852841436670.7664205082163.01092621398-1.500837354153.914781376840.006970761024430.01412389070120.0435829035050.0720656231601-0.116217399624-0.152233225519-0.2649486402550.3537271071590.1423592153230.24930747829-0.05095537672730.03242689243670.21023759078-0.02297741538360.22790198041724.07220.4945.994
102.000037510179.48767245804-2.812580028181.99993181315-5.407414705461.9999785297-1.793544863210.415288796215-0.2362450157014.657191147562.35525062272-1.98066039033-0.734179077666-1.56948798815-0.4696432833631.01734274638-0.1499443105590.06306688273311.03335732954-0.3491853019910.5089825232769.32715.23640.127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:25 )A-1 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:75 )A26 - 75
3X-RAY DIFFRACTION3( CHAIN A AND RESID 76:128 )A76 - 128
4X-RAY DIFFRACTION4( CHAIN A AND RESID 129:163 )A129 - 163
5X-RAY DIFFRACTION5( CHAIN A AND RESID 164:214 )A164 - 214
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:59 )B1 - 59
7X-RAY DIFFRACTION7( CHAIN B AND RESID 60:119 )B60 - 119
8X-RAY DIFFRACTION8( CHAIN B AND RESID 120:134 )B120 - 134
9X-RAY DIFFRACTION9( CHAIN B AND RESID 135:216 )B135 - 216
10X-RAY DIFFRACTION10( CHAIN B AND RESID 306:306 )B306

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