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- PDB-45as: Crystal structure of C11 nanobody in complex with human MR1-Ac-6-FP -

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Basic information

Entry
Database: PDB / ID: 45as
TitleCrystal structure of C11 nanobody in complex with human MR1-Ac-6-FP
Components
  • Beta-2-microglobulin
  • C11 nanoody
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / nanobody / MR1 / metabolite presentation
Function / homology
Function and homology information


antigen processing and presentation of exogenous antigen / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / MHC class I receptor activity / T cell differentiation in thymus / beta-2-microglobulin binding / T cell receptor binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...antigen processing and presentation of exogenous antigen / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / MHC class I receptor activity / T cell differentiation in thymus / beta-2-microglobulin binding / T cell receptor binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / negative regulation of neurogenesis / antigen processing and presentation of exogenous peptide antigen via MHC class II / specific granule lumen / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / tertiary granule lumen / Modulation by Mtb of host immune system / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / early endosome membrane / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / focal adhesion / lysosomal membrane / 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 exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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-30W / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE220101491 Australia
CitationJournal: Sci Immunol / Year: 2026
Title: Specific targeting of MR1-antigen complexes using nanobodies.
Authors: Hussain, H.S. / Redmond, S.J. / Awad, W. / Xu, C. / Soliman, C. / Wang, H. / Zhang, Y. / Ciacchi, L. / Gonzalez, A.P. / Mak, J.Y.W. / Fairlie, D.P. / McCluskey, J. / Corbett, A.J. / Uldrich, ...Authors: Hussain, H.S. / Redmond, S.J. / Awad, W. / Xu, C. / Soliman, C. / Wang, H. / Zhang, Y. / Ciacchi, L. / Gonzalez, A.P. / Mak, J.Y.W. / Fairlie, D.P. / McCluskey, J. / Corbett, A.J. / Uldrich, A.P. / Rossjohn, J. / Godfrey, D.I. / Koay, H.F. / Gherardin, N.A.
History
DepositionAug 21, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: C11 nanoody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0654
Polymers57,8323
Non-polymers2331
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-18 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.498, 118.498, 159.061
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Space group name HallP322(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z

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Components

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Antibody C11 nanoody


Mass: 14240.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin


Mass: 233.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 5.57 Å3/Da / Density % sol: 77.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: salt / Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953726 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953726 Å / Relative weight: 1
ReflectionResolution: 3.14→47.51 Å / Num. obs: 43262 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 118.54 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.26
Reflection shellResolution: 3.14→3.18 Å / Num. unique obs: 1557 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→47.51 Å / SU ML: 0.469 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.4806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2237 3826 8.87 %
Rwork0.2082 39326 -
obs0.2097 43152 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.47 Å2
Refinement stepCycle: LAST / Resolution: 3.14→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 16 19 3727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273809
X-RAY DIFFRACTIONf_angle_d0.55285190
X-RAY DIFFRACTIONf_chiral_restr0.0417552
X-RAY DIFFRACTIONf_plane_restr0.004686
X-RAY DIFFRACTIONf_dihedral_angle_d16.61871322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.180.34711310.40291340X-RAY DIFFRACTION92.17
3.18-3.220.34681320.35811435X-RAY DIFFRACTION98.55
3.22-3.270.34741340.35631513X-RAY DIFFRACTION98.98
3.27-3.310.36361420.33441456X-RAY DIFFRACTION99.19
3.31-3.360.36321430.30741448X-RAY DIFFRACTION98.76
3.36-3.420.30231450.30561467X-RAY DIFFRACTION98.9
3.42-3.470.30141500.2871423X-RAY DIFFRACTION98.81
3.47-3.530.33441340.26561436X-RAY DIFFRACTION98.56
3.53-3.60.28541400.24371456X-RAY DIFFRACTION98.58
3.6-3.660.26761370.24831469X-RAY DIFFRACTION99.38
3.66-3.740.25871500.24711476X-RAY DIFFRACTION99.57
3.74-3.820.2671530.25371474X-RAY DIFFRACTION99.63
3.82-3.910.26511320.20681460X-RAY DIFFRACTION99.62
3.91-4.010.26131460.20321442X-RAY DIFFRACTION99.81
4.01-4.120.24541350.18021483X-RAY DIFFRACTION99.69
4.12-4.240.18441500.17851470X-RAY DIFFRACTION99.69
4.24-4.370.19681380.16731442X-RAY DIFFRACTION99.75
4.37-4.530.19381520.17481477X-RAY DIFFRACTION99.51
4.53-4.710.1731460.16781447X-RAY DIFFRACTION100
4.71-4.920.19331500.14971478X-RAY DIFFRACTION99.57
4.93-5.180.15661350.1761474X-RAY DIFFRACTION99.75
5.18-5.510.24531440.19581469X-RAY DIFFRACTION99.81
5.51-5.930.1971440.21341465X-RAY DIFFRACTION99.57
5.93-6.530.26451500.21871448X-RAY DIFFRACTION99.38
6.53-7.470.21761330.20821452X-RAY DIFFRACTION97.78
7.47-9.390.1821400.17981465X-RAY DIFFRACTION100
9.42-47.510.19771400.20881461X-RAY DIFFRACTION98.58
Refinement TLS params.Method: refined / Origin x: -13.36520669 Å / Origin y: 44.6144735145 Å / Origin z: 26.2382311071 Å
111213212223313233
T0.942612418857 Å2-0.187553982008 Å2-0.0489696483663 Å2-0.606839089042 Å20.0241686140754 Å2--0.714497966983 Å2
L0.290394983072 °2-0.0926310066735 °2-0.140920801291 °2-0.760222835252 °20.332759119569 °2--0.807307591673 °2
S-0.161257719685 Å °0.153701744566 Å °-0.0951240572492 Å °0.182295742432 Å °0.245685298472 Å °0.0108158067738 Å °0.0779329180063 Å °-0.180141098418 Å °0.0925954752951 Å °
Refinement TLS groupSelection details: all

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