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- PDB-45ar: Crystal structure of C11 nanobody in complex with human MR1-5-OP-RU -

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Basic information

Entry
Database: PDB / ID: 45ar
TitleCrystal structure of C11 nanobody in complex with human MR1-5-OP-RU
Components
  • Beta-2-microglobulin
  • C11 nanobody
  • 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-2LJ / 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 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 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1715
Polymers57,8323
Non-polymers3392
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-36 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.455, 208.455, 77.672
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 2 types, 2 molecules AB

#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

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Antibody , 1 types, 1 molecules C

#3: Antibody C11 nanobody


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)

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Non-polymers , 3 types, 164 molecules

#4: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 162 / 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: 8.44 Å3/Da / Density % sol: 85.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953723 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953723 Å / Relative weight: 1
ReflectionResolution: 3→47.57 Å / Num. obs: 75063 / % possible obs: 99.35 % / Redundancy: 3.5 % / Biso Wilson estimate: 65.12 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1236 / Net I/σ(I): 8.92
Reflection shellResolution: 3→3.04 Å / Num. unique obs: 2673 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.57 Å / SU ML: 0.3462 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 3835 5.11 %
Rwork0.1883 71174 -
obs0.1894 75009 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.54 Å2
Refinement stepCycle: LAST / Resolution: 3→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 23 162 4018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00144039
X-RAY DIFFRACTIONf_angle_d0.41895495
X-RAY DIFFRACTIONf_chiral_restr0.0396575
X-RAY DIFFRACTIONf_plane_restr0.0031730
X-RAY DIFFRACTIONf_dihedral_angle_d12.30681451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.36531330.33732539X-RAY DIFFRACTION96.92
3.04-3.080.28711420.31252617X-RAY DIFFRACTION98.85
3.08-3.120.36581440.32674X-RAY DIFFRACTION98.22
3.12-3.170.34251340.28142618X-RAY DIFFRACTION99.71
3.17-3.210.32781400.27592689X-RAY DIFFRACTION99.93
3.21-3.260.32321400.26022606X-RAY DIFFRACTION99.93
3.26-3.320.2991420.24252651X-RAY DIFFRACTION99.79
3.32-3.370.31171520.22562690X-RAY DIFFRACTION99.75
3.37-3.440.23061380.2292597X-RAY DIFFRACTION99.71
3.44-3.50.22681460.21812645X-RAY DIFFRACTION99.93
3.5-3.570.20541480.21132649X-RAY DIFFRACTION100
3.57-3.650.18771480.22352651X-RAY DIFFRACTION99.43
3.65-3.740.25531370.22062599X-RAY DIFFRACTION98.49
3.74-3.830.21641460.20262619X-RAY DIFFRACTION99.64
3.83-3.930.26461340.24132601X-RAY DIFFRACTION96.57
3.93-4.050.19261420.16722633X-RAY DIFFRACTION99.71
4.05-4.180.15271420.15172627X-RAY DIFFRACTION99.86
4.18-4.330.18261400.14242697X-RAY DIFFRACTION100
4.33-4.50.16071420.14142630X-RAY DIFFRACTION99.89
4.5-4.70.14131460.13332633X-RAY DIFFRACTION99.96
4.71-4.950.14971400.13072678X-RAY DIFFRACTION99.86
4.95-5.260.1671440.13782654X-RAY DIFFRACTION99.89
5.26-5.670.17481500.15612642X-RAY DIFFRACTION99.75
5.67-6.240.20061280.16722582X-RAY DIFFRACTION97.45
6.24-7.130.15311450.19262654X-RAY DIFFRACTION99.96
7.14-8.980.16991440.16992658X-RAY DIFFRACTION100
8.98-47.570.25331480.1752641X-RAY DIFFRACTION99.36
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)
10.174498624768280.0071013304297841-0.125263517214720.00299298261019460.00304075812036210.091178091687582-0.247287705158680.23597278113216-0.0744326319238270.114137852505970.186175390595620.0798913516591110.23049886715312-0.090300438113553-0.0270366499590630.72043845468609-0.019917066738866-0.0897403230207090.311358361225880.0326383183661660.40996588355375-104.2408691901931.987633765237-16.834739187072
20.24857195469274-0.094571516992164-0.159702511821210.239244879407630.112322980553890.456390532092740.06938847213929-0.163423833493810.15554813792169-0.00248494983457330.13555871709705-0.0878005398581270.424962957175520.249337726174660.78663557486870.328107261227990.062523397361839-0.057187862844025-0.0324890968892420.0846397894956560.15016727421572-101.6734315015439.861894087539-14.371600692208
30.26366457889913-0.012768575367584-0.118650828721870.0766884069335930.0332893676942980.0703251487772750.091713739042462-0.0263206640785830.0498455877499670.0359949567345310.095854254899654-0.0992065826216360.410235497604810.0329133481978070.0553792544644770.910203345823630.14428091033771-0.0654336286407540.365744917293520.0336132613838830.39041732849822-96.21598095405724.365533652213-1.5695506644462
40.103387431690550.000402106842353790.0478210121405660.000166397743098090.000851137795539860.0230111501930810.0726455093708880.169361411675830.071767377760937-0.0096695665836803-0.127617791559730.08058797526928-0.00556921185582720.049842735652259-0.00826459420655091.5531399156669-0.08183780732419-0.0241552962520070.47156196790118-0.00983280354816160.73130794315363-89.8905694796041.5297117163442-23.239369782594
50.14343521061928-0.106039062782840.152753818910970.420693804117250.263088347075340.58615556164127-0.215743002873650.049356636771996-0.06421935553552-0.0944940208531780.46024594273704-0.20160146727012-0.243296998852020.0355141303417380.0591134858172161.4498785121158-0.0465622277009470.050258193118680.43952915644739-0.0145000564795480.83643424995801-84.9153153116337.8186838224205-19.874551996452
60.357062889725790.00339410462328-0.047766973765030.0052351192711010.0187723586093540.088156853471976-0.0500394422030140.060974814999123-0.296776930915630.0084758990508582-0.0104736638381720.00542135775715980.20146687490324-0.035903220313988-0.108309231348861.1659405581852-0.063707987613897-0.129883865067870.15335577194751-0.101258474873420.35361561102088-103.850425277316.173803313257-26.433109088127
70.00649220310857930.00108544520293930.00188458283880820.008256984682847-0.0110692799155570.0145430474032740.00483181121303010.00363879117944570.034473407900833-0.031845182466183-0.039797023821869-0.0689706377413180.022551726634598-0.0157442878235345.0925613147467E-71.601491287647-0.25699365095596-0.188127076596560.63500783201733-0.0500285862614690.77518808990469-115.6429844569212.078562237647-28.466364316315
80.0063273455371739-0.019156569231824-0.00706065772122720.0521696490828780.0203067480117890.043813020568306-0.013331503015163-0.0238110332941250.0200442113135570.089223700978013-0.093207522747952-0.0252516442554280.10129867950939-0.015611750176404-0.124997704337110.916324000683560.0029978396616689-0.0793483181592340.175434036588850.0253945902785290.52550240093742-102.6286189788826.72376371002-21.562992425702
90.0419658340906060.0045030550555579-0.0222006046793960.017697533932182-0.0136359487204250.022390497446237-0.023647325108490.0012878208386902-0.0445245419465760.0018148601394888-0.057761987083693-0.015598250747084-0.0304776634795090.001726033874845-0.0331764061474091.2410418754626-0.39712820362769-0.0630756155571920.41936840982386-0.005078416195220.71080310012686-111.459500071628.3455102548972-21.724378237888
100.00134414227281520.00136960272628550.00218230931426740.00148678837890860.00121679559673520.00256406933961340.0280007919178020.0480724557207370.00061995887647332-0.0068412310241257-0.018889433890933-0.0078513313744828-0.00926571776603880.02411408397864-2.9160537746073E-61.5713300608575-0.26857438101326-0.0865539284918240.980743985409750.0885144349172081.4444473908214-109.80297994723-2.6266717494432-30.971462418721
110.00242025926583260.00324620224035680.00223595823649680.00170779501092740.00113774174376760.011281830542642-0.000868119682241640.065611810386160.0541268540344030.0082521535478554-0.012604728567817-0.0116424117256090.054689074125605-0.0366112094844392.3715758206103E-51.6359873915606-0.11158374419432-0.129067936378680.54526718323827-0.0186011424539320.76238361063203-109.0613605124318.921305531237-35.902116054843
12-0.00112140717341870.00224713957327990.000655522432878040.00791942298113330.00746655461284680.0075588005464648-0.14931155887168-0.10187166363503-0.19399873662271-0.0086823539461687-0.15715273223870.0037077083733390.0134144309438780.028821785398369-6.5935315513367E-51.30196916821280.083046764273440.0189673098971930.60332070362283-0.0181912855715540.76324877696116-103.360953697417.1818891716276-32.798316379471
130.0028306509363117-0.0057106795057733-0.00188949001698740.00657756618896290.00369784317733830.014647724631483-0.068853103932872-0.0756740435678170.057399150127007-0.0204141038750150.06404990949983-0.12265477702727-0.039568015231285-0.332357581749569.9684291462387E-60.45692251647112-0.026074724618910.0242563206725510.72707059728425-0.0726063596018890.61302071707079-117.3711644872660.7042990781147.0606211730813
140.0447863350030460.00794869605997570.0064546925845220.0347496028106330.0398868871305780.0299073754830030.10641689075788-0.273865638526970.0766405877339380.160497957598530.00025591736866742-0.256743622315420.10212892700605-0.133937018726876.0557880318459E-50.57163742394591-0.0382780351717950.0276481199645370.522735488023150.000386665051713530.51238520092599-111.4379735465149.921090910693.1830409715641
150.014441850047069-0.0045221866933368-0.0151996942572550.0296219798282510.00858742234351060.0107250047027890.03757381485833-0.0222704439828710.094066522786655-0.0093779957418790.073491974296509-0.287927002613090.0219944181085750.0242143446532653.096111680474E-50.52959598737127-0.047053505739122-0.0125416681665510.548041025566930.00149351379953270.57270720815853-117.2985806375647.793220246747-1.5414416973997
160.049766899384219-0.026767500706031-0.00213655796927030.0172312347879220.0228999204265030.05982270470164-0.05945577684881-0.099115267672807-0.00938381580897580.0656434605520890.011605317296331-0.0419825016673540.25055276319562-0.226089630005211.3646776026548E-60.343959143496830.0222664685783570.0101018648894050.46362674496078-0.0479598145449880.35433592329364-116.1090663389651.9757908004873.7323685177756
170.00864611751619090.00219044526776350.00697137523233920.000646144457132240.00329342179101360.0146185126377840.0738636649527550.010677529800973-0.0300881276381860.0953549636124880.0491174213084740.0195245924995740.06322476259790.00038053084563351-4.1975567171222E-50.461183950835680.163552520321490.0613735279786721.0110590298374-0.0426611013058720.59335077708601-125.4100727661359.11018854587917.282206498714
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 21 )AA0 - 211 - 22
22chain 'A' and (resid 22 through 158 )AA22 - 15823 - 159
33chain 'A' and (resid 159 through 182 )AA159 - 182160 - 183
44chain 'A' and (resid 183 through 205 )AA183 - 205184 - 201
55chain 'A' and (resid 206 through 270 )AA206 - 270202 - 259
66chain 'B' and (resid 0 through 35 )BC0 - 351 - 36
77chain 'B' and (resid 36 through 51 )BC36 - 5137 - 52
88chain 'B' and (resid 52 through 65 )BC52 - 6553 - 66
99chain 'B' and (resid 66 through 71 )BC66 - 7167 - 72
1010chain 'B' and (resid 72 through 77 )BC72 - 7773 - 78
1111chain 'B' and (resid 78 through 90 )BC78 - 9079 - 91
1212chain 'B' and (resid 91 through 98 )BC91 - 9892 - 99
1313chain 'C' and (resid 2 through 23 )CD2 - 231 - 22
1414chain 'C' and (resid 24 through 44 )CD24 - 4423 - 43
1515chain 'C' and (resid 45 through 60 )CD45 - 6044 - 59
1616chain 'C' and (resid 61 through 113 )CD61 - 11360 - 112
1717chain 'C' and (resid 114 through 122 )CD114 - 122113 - 121

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