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- PDB-8rwb: Crystal structure of ULBP6 in complex with a blocking antibody -

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Basic information

Entry
Database: PDB / ID: 8rwb
TitleCrystal structure of ULBP6 in complex with a blocking antibody
Components
  • Heavy chain
  • Light chain
  • UL16-binding protein 6
KeywordsIMMUNE SYSTEM / FAB
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of T cell mediated cytotoxicity / immune response / external side of plasma membrane / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein
Similarity search - Domain/homology
UL16-binding protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.307 Å
AuthorsBharill, S. / Chen, I. / Ivic, N. / Bahrami Dizicheh, Z. / Wu, Y. / Doamekpor, S. / Koenig, P. / Fuh, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of ULBP6 in complex with a blocking antibody
Authors: Bharill, S. / Chen, I. / Ivic, N. / Bahrami Dizicheh, Z. / Wu, Y. / Doamekpor, S. / Koenig, P. / Fuh, G.
History
DepositionFeb 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: UL16-binding protein 6
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6279
Polymers65,7043
Non-polymers9246
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-7 kcal/mol
Surface area25170 Å2
Unit cell
Length a, b, c (Å)106.551, 95.803, 97.203
Angle α, β, γ (deg.)90.000, 117.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules P

#1: Protein UL16-binding protein 6 / Retinoic acid early transcript 1L protein


Mass: 19719.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAET1L, ULBP6 / Production host: Homo sapiens (human) / References: UniProt: Q5VY80

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain


Mass: 22896.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#3: Antibody Light chain


Mass: 23087.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 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.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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 , 3 types, 138 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Glycerol 10.0 %v/v MES: 0.10 M pH:6.00 PEG 1K 5.0 %w/v PEG 600 30.0 %w/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.307→86.031 Å / Num. obs: 19970 / % possible obs: 92.3 % / Redundancy: 4 % / CC1/2: 0.991 / Net I/σ(I): 7.2
Reflection shellResolution: 2.307→2.658 Å / Num. unique obs: 999 / CC1/2: 0.581

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.307→86.031 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.852 / SU B: 12.238 / SU ML: 0.277 / Cross valid method: FREE R-VALUE / ESU R Free: 0.421
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2865 1006 5.038 %
Rwork0.2159 18964 -
all0.219 --
obs-19970 52.373 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.673 Å2-0 Å20.182 Å2
2---0.988 Å2-0 Å2
3---0.079 Å2
Refinement stepCycle: LAST / Resolution: 2.307→86.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 60 134 4811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134812
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174346
X-RAY DIFFRACTIONr_ext_dist_refined_d0.4430.055
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6566561
X-RAY DIFFRACTIONr_angle_other_deg1.0691.58410051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3855.146618
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg0.776203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95323.209215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51115.118765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7611519
X-RAY DIFFRACTIONr_chiral_restr0.0460.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025501
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021091
X-RAY DIFFRACTIONr_nbd_refined0.1510.2747
X-RAY DIFFRACTIONr_symmetry_nbd_other0.150.24010
X-RAY DIFFRACTIONr_nbtor_refined0.1470.22174
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.22221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2121
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.24
X-RAY DIFFRACTIONr_nbd_other0.1510.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.25
X-RAY DIFFRACTIONr_mcbond_it1.7694.6112430
X-RAY DIFFRACTIONr_mcbond_other1.7624.6092429
X-RAY DIFFRACTIONr_mcangle_it3.1166.9083042
X-RAY DIFFRACTIONr_mcangle_other3.1166.913043
X-RAY DIFFRACTIONr_scbond_it1.4014.6222382
X-RAY DIFFRACTIONr_scbond_other1.4014.6222383
X-RAY DIFFRACTIONr_scangle_it2.5086.8933517
X-RAY DIFFRACTIONr_scangle_other2.5086.8933518
X-RAY DIFFRACTIONr_lrange_it5.1551.2974891
X-RAY DIFFRACTIONr_lrange_other5.14951.34892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.307-2.3670.53830.37520.37828000.140.7081.96430.357
2.367-2.4320.63170.3831020.39627180.3860.6514.01030.385
2.432-2.5020.4460.3351830.33926640.6080.6597.09460.335
2.502-2.5790.315170.3222650.32225940.7760.74510.87120.31
2.579-2.6640.364170.3183820.3225210.6930.72315.82710.309
2.664-2.7570.437350.3244640.33224090.7320.74120.7140.303
2.757-2.8610.447360.2996730.30623600.6730.78930.04240.281
2.861-2.9780.378440.2958850.29922390.7270.78841.49170.277
2.978-3.110.38590.27512740.2821710.7750.80661.40030.25
3.11-3.2610.31910.2818190.28120690.7920.81192.31510.26
3.261-3.4380.3281030.25818490.26119590.7950.84899.64270.236
3.438-3.6460.306960.22417690.22818680.8540.88799.83940.208
3.646-3.8970.288870.21716550.22117420.8760.9051000.197
3.897-4.2080.2521010.1915470.19416490.9090.92999.93940.178
4.208-4.6090.233700.1714200.17314910.9310.94799.93290.16
4.609-5.1510.229620.16713070.1713720.9370.94899.78130.161
5.151-5.9450.267580.19911570.20312160.9220.92799.91780.192
5.945-7.2720.32680.2049500.21110190.8850.91699.90190.196
7.272-10.2480.242300.1557720.1588080.9310.95499.25740.165
10.248-86.0310.204160.2174390.2174610.9610.94198.69850.241

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