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- PDB-6v7z: Human CD1d presenting alpha-Galactosylceramide in complex with VH... -

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Basic information

Entry
Database: PDB / ID: 6v7z
TitleHuman CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
  • Nanobody VHH ID22
KeywordsIMMUNE SYSTEM / lipid / nanobody
Function / homology
Function and homology information


lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / detection of bacterium / positive regulation of T cell proliferation / cell adhesion molecule binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / histone binding / T cell differentiation in thymus / protein refolding / basolateral plasma membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
MHC-I family domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...MHC-I family domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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
Similarity search - Domain/homology
Chem-AGH / beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsShahine, A. / Rossjohn, J.
CitationJournal: Nat Cancer / Year: 2020
Title: A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.
Authors: Shahine, A. / Rossjohn, J.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
E: Nanobody VHH ID22
F: Nanobody VHH ID22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,34120
Polymers127,9326
Non-polymers4,41014
Water1,15364
1
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
F: Nanobody VHH ID22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,37712
Polymers63,9663
Non-polymers2,4119
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
E: Nanobody VHH ID22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9648
Polymers63,9663
Non-polymers1,9985
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.717, 121.933, 172.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 6 and (name N or name...
21(chain C and ((resid 6 and (name N or name...
12(chain B and ((resid 1 through 2 and (name N...
22(chain D and ((resid 1 through 2 and (name N...
13(chain E and (resid 1 through 2 or (resid 3...
23(chain F and ((resid 1 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 6 and (name N or name...A6
121(chain A and ((resid 6 and (name N or name...A4 - 289
131(chain A and ((resid 6 and (name N or name...A4 - 289
141(chain A and ((resid 6 and (name N or name...A4 - 289
151(chain A and ((resid 6 and (name N or name...A4 - 289
211(chain C and ((resid 6 and (name N or name...C6
221(chain C and ((resid 6 and (name N or name...C6 - 277
231(chain C and ((resid 6 and (name N or name...C6 - 277
241(chain C and ((resid 6 and (name N or name...C6 - 277
251(chain C and ((resid 6 and (name N or name...C6 - 277
112(chain B and ((resid 1 through 2 and (name N...B1 - 2
122(chain B and ((resid 1 through 2 and (name N...B0 - 98
132(chain B and ((resid 1 through 2 and (name N...B0 - 98
142(chain B and ((resid 1 through 2 and (name N...B0 - 98
152(chain B and ((resid 1 through 2 and (name N...B0 - 98
212(chain D and ((resid 1 through 2 and (name N...D1 - 2
222(chain D and ((resid 1 through 2 and (name N...D1 - 97
232(chain D and ((resid 1 through 2 and (name N...D1 - 97
242(chain D and ((resid 1 through 2 and (name N...D1 - 97
252(chain D and ((resid 1 through 2 and (name N...D1 - 97
113(chain E and (resid 1 through 2 or (resid 3...E1 - 2
123(chain E and (resid 1 through 2 or (resid 3...E3
133(chain E and (resid 1 through 2 or (resid 3...E1 - 117
143(chain E and (resid 1 through 2 or (resid 3...E1 - 117
153(chain E and (resid 1 through 2 or (resid 3...E1 - 117
213(chain F and ((resid 1 and (name N or name...F1
223(chain F and ((resid 1 and (name N or name...F1 - 117
233(chain F and ((resid 1 and (name N or name...F1 - 117
243(chain F and ((resid 1 and (name N or name...F1 - 117
253(chain F and ((resid 1 and (name N or name...F1 - 117

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 39471.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769

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Antibody , 1 types, 2 molecules EF

#3: Antibody Nanobody VHH ID22


Mass: 12614.919 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMEK219 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1

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Sugars , 6 types, 8 molecules

#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.: 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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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
#7: 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
#8: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9 / Feature type: SUBJECT OF INVESTIGATION
#12: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 70 molecules

#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#13: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 29% (v/v) PEG3350, 0.2M ammonium sulphate, 0.1M Bis-Tris (pH 5.3), 3% (v/v) glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.75→48.78 Å / Num. obs: 37944 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rpim(I) all: 0.0036 / Net I/σ(I): 12.8
Reflection shellResolution: 2.75→2.87 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4554 / CC1/2: 0.842 / Rpim(I) all: 0.0328 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PO6, 3P0G

2po6

3p0g


Resolution: 2.75→45.309 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.22
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1860 4.91 %RANDOM
Rwork0.1859 ---
obs0.1891 37863 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.9 Å2 / Biso mean: 78.8145 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.75→45.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7525 0 294 66 7885
Biso mean--85.42 65.4 -
Num. residues----967
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2038X-RAY DIFFRACTION9.137TORSIONAL
12C2038X-RAY DIFFRACTION9.137TORSIONAL
21B809X-RAY DIFFRACTION9.137TORSIONAL
22D809X-RAY DIFFRACTION9.137TORSIONAL
31E929X-RAY DIFFRACTION9.137TORSIONAL
32F929X-RAY DIFFRACTION9.137TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.75-2.82440.36041330.2742748
2.8244-2.90740.35371510.26732710
2.9074-3.00130.34761480.24642709
3.0013-3.10850.33841390.24372733
3.1085-3.23290.32391500.23852732
3.2329-3.380.31961460.21162752
3.38-3.55820.25221270.19252750
3.5582-3.7810.26831330.18272769
3.781-4.07280.20881330.1692759
4.0728-4.48230.19021680.14052757
4.4823-5.13010.17531270.12982813
5.1301-6.46040.23451370.18282825
6.4604-45.3090.2811680.20532946
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)
13.1097-0.53860.02342.45860.76666.9167-0.2648-0.26740.17760.01810.27240.3885-0.1753-0.6903-0.00430.35520.027-0.04090.37980.07340.46154.364-6.733-21.841
23.50870.90461.70031.6319-0.1493.0528-0.0266-0.2627-0.03980.1665-0.15-0.2467-0.02370.33480.15220.46940.065-0.0180.36420.05520.396332.348-6.719-2.988
32.69350.76070.65195.07060.78743.50990.1846-0.422-0.58870.5964-0.0239-0.3640.4217-0.0847-0.11690.43750.0281-0.02980.37120.10220.5322.134-22.514-5.857
40.8610.51330.71013.40491.31384.4795-0.3001-0.47110.12620.23250.02280.12590.14240.35810.26840.46880.21320.05720.7297-0.0850.44622.938-41.073-32.645
54.3642-0.591-1.13553.92110.71985.1465-0.0969-0.60240.1614-0.19030.0805-0.4153-0.17880.8096-0.02270.42630.0562-0.00820.4701-0.08550.37329.925-40.892-45.077
63.60431.5153-1.27371.123-0.27031.4918-0.4466-0.7199-0.52420.26470.36670.29030.435-0.59790.08520.88230.24570.33451.1340.28250.798515.13-63.419-22.885
75.9798-0.7144-4.27614.74082.03377.5264-0.00960.38170.1111-0.0988-0.0314-0.1404-0.1336-0.3210.02120.515-0.0644-0.14460.3803-0.02890.43124.888-50.15-67.874
84.788-0.3334-1.80113.9015-1.12339.5375-0.2440.7013-0.0417-0.56090.6758-0.15490.1751-0.0212-0.37220.6191-0.2389-0.07460.5877-0.05290.527414.09-12.866-52.446
92.1997-0.747-0.00293.08810.02241.799-0.9343-1.1285-0.70830.41770.74970.29560.54080.04290.17951.07520.55350.30961.180.27820.862834.89-68.699-17.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:174 )A4 - 174
2X-RAY DIFFRACTION2( CHAIN A AND RESID 175:278 )A175 - 278
3X-RAY DIFFRACTION3( CHAIN B AND RESID 0:98 )B0 - 98
4X-RAY DIFFRACTION4( CHAIN C AND RESID 6:107 )C6 - 107
5X-RAY DIFFRACTION5( CHAIN C AND RESID 109:169 )C109 - 169
6X-RAY DIFFRACTION6( CHAIN D AND RESID 1:97 )D1 - 97
7X-RAY DIFFRACTION7( CHAIN E AND RESID 1:117 )E1 - 117
8X-RAY DIFFRACTION8( CHAIN F AND RESID 1:117 )F1 - 117
9X-RAY DIFFRACTION9( CHAIN C AND RESID 170:277 )C170 - 277

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