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- PDB-8f8x: Crystal structure of Nb.X0 bound to the afucosylated human IgG1 f... -

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Basic information

Entry
Database: PDB / ID: 8f8x
TitleCrystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form II
Components
  • Nb.X0
  • Uncharacterized protein DKFZp686C11235
KeywordsIMMUNE SYSTEM / nanobody / glycobiology / immunoglobulin
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelidae mixed library (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGoldgur, Y. / Ravetch, J. / Gupta, A. / Kao, K. / Oren, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007739 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI111825 United States
Bill & Melinda Gates FoundationINV-034057 United States
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody.
Authors: Gupta, A. / Kao, K.S. / Yamin, R. / Oren, D.A. / Goldgur, Y. / Du, J. / Lollar, P. / Sundberg, E.J. / Ravetch, J.V.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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: Uncharacterized protein DKFZp686C11235
B: Uncharacterized protein DKFZp686C11235
C: Nb.X0
D: Nb.X0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5616
Polymers76,9274
Non-polymers2,6342
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.577, 92.233, 76.497
Angle α, β, γ (deg.)90.000, 117.040, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 238 through 507)
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROLEUA1 - 206
d_12ens_1NAGNAGE
d_13ens_1NAGNAGE
d_14ens_1BMABMAE
d_15ens_1MANMANE
d_16ens_1NAGNAGE
d_17ens_1MANMANE
d_18ens_1NAGNAGE
d_21ens_1PROLEUB2 - 207
d_22ens_1NAGNAGF
d_23ens_1NAGNAGF
d_24ens_1BMABMAF
d_25ens_1MANMANF
d_26ens_1NAGNAGF
d_27ens_1MANMANF
d_28ens_1NAGNAGF
d_11ens_2GLNSERC1 - 120
d_21ens_2GLNSERD1 - 120

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.552122179636, -0.0598123333131, -0.831615045281), (-0.0171774145993, -0.996395807705, 0.083068229878), (-0.833586249396, 0.0601488085586, 0.549104803883)49.4840837876, -1.81769719896, 28.121455165
2given(-0.494686543479, -0.0882965361902, -0.864574430224), (0.0675365820024, -0.99572275121, 0.0630477026881), (-0.866443324051, -0.027201551787, 0.498533892316)49.9605564753, -2.99152906346, 25.4796098714

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Components

#1: Protein Uncharacterized protein DKFZp686C11235


Mass: 25357.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7
#2: Antibody Nb.X0


Mass: 13105.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1317.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v PEG 6000, 0.1 M Sodium citrate 4.0, 0.2 M Lithium chloride. No additional cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21352 / % possible obs: 90.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 65.07 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.05 / Net I/σ(I): 23.6
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 1051 / CC1/2: 0.504 / Rpim(I) all: 0.574

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.12 Å / SU ML: 0.4459 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.3889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2853 2019 9.46 %
Rwork0.2147 19321 -
obs0.2214 21340 88.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5164 0 178 15 5357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01455478
X-RAY DIFFRACTIONf_angle_d1.79037448
X-RAY DIFFRACTIONf_chiral_restr0.0779846
X-RAY DIFFRACTIONf_plane_restr0.0147936
X-RAY DIFFRACTIONf_dihedral_angle_d7.8675825
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.51500159136
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.2326121974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.45421260.35321150X-RAY DIFFRACTION74.88
2.66-2.740.37831500.3281397X-RAY DIFFRACTION91.38
2.74-2.820.33951370.29441442X-RAY DIFFRACTION91.8
2.82-2.910.43861570.31491402X-RAY DIFFRACTION92.03
2.91-3.010.36921470.28381417X-RAY DIFFRACTION91.52
3.01-3.130.36791460.27171420X-RAY DIFFRACTION91.53
3.13-3.280.32621430.2561403X-RAY DIFFRACTION90.73
3.28-3.450.35351380.24921395X-RAY DIFFRACTION89.7
3.45-3.660.31271480.22691393X-RAY DIFFRACTION89.91
3.66-3.950.28191460.21781384X-RAY DIFFRACTION89.26
3.95-4.340.26231470.19441393X-RAY DIFFRACTION88.61
4.34-4.970.19951460.1651352X-RAY DIFFRACTION88.07
4.97-6.260.27391420.18631400X-RAY DIFFRACTION88.82
6.26-46.120.23461460.17531373X-RAY DIFFRACTION86.01
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)
12.891417847060.0582597884314-2.102246254322.597108576821.593332129075.2796909252-0.204589519972-0.2614486029450.449706019002-0.2673555050450.184292768336-0.0714734036653-0.53959688867-0.09323613038710.02500901848390.5315911615390.168350927022-0.09064465666020.4139209314510.07624836280920.5960760877133.64410.44110.606
22.380279938571.56524021923-1.243456920371.24585215796-1.328430744855.05160832728-0.3767167960730.04653378153460.251466299699-0.4540760143480.1716404379290.1417542554140.418997573564-0.4412085715740.2100040031190.6784664247480.129624319762-0.09804815738820.390949523972-0.05037235484670.59771956145321.48-11.1276.553
34.005044673850.4808337441772.048770364826.25927748142-0.03985201837895.590826619930.1368683436710.615641541791-0.306172477090.155789172544-0.13804088663-0.276286626846-0.2126889923940.2069569184120.007347869459710.342547690513-0.02052064379690.136415305610.557783318589-0.0972017045080.30692934302235.307-9.02644.9
45.325178767640.492515450345-0.9424692373485.467064609221.277582068165.365204745990.243007165083-0.00763240852524-1.27101272737-0.6896008144860.196602055180.6181552849471.334104606370.0716332265203-0.2616950124790.7412270955130.159501365737-0.2427349232890.492739707124-0.09411239900730.970938949119-5.46212.01417.568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 238:443 )A238 - 443
2X-RAY DIFFRACTION2( CHAIN B AND RESID 237:443 )B237 - 443
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:120 )C1 - 120
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:120 )D1 - 120

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