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- PDB-6ss4: Structure of arginase-2 in complex with the inhibitory human anti... -

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Basic information

Entry
Database: PDB / ID: 6ss4
TitleStructure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0021181
Components
  • Arginase-2, mitochondrial
  • Fab C0021181 heavy chain (IgG1)
  • Fab C0021181 light chain (IgG1)
KeywordsPROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment
Function / homology
Function and homology information


negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginine catabolic process to ornithine ...negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginine catabolic process to ornithine / arginase / arginase activity / urea cycle / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-17 production / regulation of reactive oxygen species biosynthetic process / ureteric bud development / negative regulation of tumor necrosis factor production / striated muscle contraction / nitric oxide biosynthetic process / positive regulation of cellular senescence / manganese ion binding / adaptive immune response / mitochondrial matrix / innate immune response / mitochondrion / cytoplasm
Similarity search - Function
Arginase / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Arginase-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBurschowsky, D. / Addyman, A. / Fiedler, S. / Groves, M. / Haynes, S. / Seewooruthun, C. / Carr, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC1362/A20263 United Kingdom
CitationJournal: Mabs
Title: Structural and functional characterization of C0021158, a high-affinity monoclonal antibody that inhibits Arginase 2 function via a novel non-competitive mechanism of action.
Authors: Austin, M. / Burschowsky, D. / Chan, D.T.Y. / Jenkinson, L. / Haynes, S. / Diamandakis, A. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / ...Authors: Austin, M. / Burschowsky, D. / Chan, D.T.Y. / Jenkinson, L. / Haynes, S. / Diamandakis, A. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / Hadjinicolaou, A.V. / Gileadi, U. / Gowans, E. / Shibata, Y. / Barnard, M. / Kaserer, T. / Sharma, P. / Luheshi, N.M. / Wilkinson, R.W. / Vaughan, T.J. / Holt, S.V. / Cerundolo, V. / Carr, M.D. / Groves, M.A.T.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
AAA: Arginase-2, mitochondrial
HHH: Fab C0021181 heavy chain (IgG1)
LLL: Fab C0021181 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2346
Polymers85,0293
Non-polymers2053
Water0
1
AAA: Arginase-2, mitochondrial
HHH: Fab C0021181 heavy chain (IgG1)
LLL: Fab C0021181 light chain (IgG1)
hetero molecules

AAA: Arginase-2, mitochondrial
HHH: Fab C0021181 heavy chain (IgG1)
LLL: Fab C0021181 light chain (IgG1)
hetero molecules

AAA: Arginase-2, mitochondrial
HHH: Fab C0021181 heavy chain (IgG1)
LLL: Fab C0021181 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,70218
Polymers255,0889
Non-polymers6159
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)150.380, 150.380, 110.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Arginase-2, mitochondrial / / Arginase II / Kidney-type arginase / Non-hepatic arginase / Type II arginase


Mass: 37084.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78540, arginase
#2: Antibody Fab C0021181 heavy chain (IgG1)


Mass: 24819.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Amino acids are numbered according to the Kabat numbering scheme.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU1.3 fab / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): ExpiCHO
#3: Antibody Fab C0021181 light chain (IgG1)


Mass: 23124.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Amino acids are numbered according to the Kabat numbering scheme. Residue 10 would not be present in the Kabat scheme, but due to problems with non-continuous numbering in L-peptides, we ...Details: Amino acids are numbered according to the Kabat numbering scheme. Residue 10 would not be present in the Kabat scheme, but due to problems with non-continuous numbering in L-peptides, we included it. Therefore, residues 2-10 should be read as 1-9, per Kabat.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU1.3 fab / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): ExpiCHO
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

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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: 4.25 Å3/Da / Density % sol: 71.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM MMT pH 5.0 (malic acid, MES, tris) 20% glycerol 10% PEG4000 15 mM NaNO3 15 mM Na2HPO4 15 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5053
pseudo-merohedral22-h,-k,l20.4947
ReflectionResolution: 2.9→44.98 Å / Num. obs: 32384 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 1 / Rmerge(I) obs: 0.35 / Net I/σ(I): 11
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 20.8 % / Rmerge(I) obs: 5.19 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4672 / CC1/2: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZE,6SS0

4hze

6ss0


Resolution: 2.9→44.98 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.176 / SU B: 25.779 / SU ML: 0.224 / Average fsc free: 0.9648 / Average fsc work: 0.981 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3181 1602 4.947 %
Rwork0.2655 30779 -
all0.268 --
obs-32381 99.975 %
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: 79.623 Å2
Baniso -1Baniso -2Baniso -3
1--14.109 Å20 Å20 Å2
2---14.109 Å20 Å2
3---28.219 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5619 0 7 0 5626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135773
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175246
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.6397853
X-RAY DIFFRACTIONr_angle_other_deg1.3791.5712210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2375743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32322.275255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.78115906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6451530
X-RAY DIFFRACTIONr_chiral_restr0.080.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026476
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021164
X-RAY DIFFRACTIONr_nbd_refined0.2230.21310
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2250.25416
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22716
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.22968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2181
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0810.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.221
X-RAY DIFFRACTIONr_nbd_other0.270.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3380.29
X-RAY DIFFRACTIONr_mcbond_it2.3863.8082981
X-RAY DIFFRACTIONr_mcbond_other2.3843.8082980
X-RAY DIFFRACTIONr_mcangle_it3.8465.7063721
X-RAY DIFFRACTIONr_mcangle_other3.8455.7073722
X-RAY DIFFRACTIONr_scbond_it2.3963.8972792
X-RAY DIFFRACTIONr_scbond_other2.3413.892788
X-RAY DIFFRACTIONr_scangle_it3.3475.824132
X-RAY DIFFRACTIONr_scangle_other3.2675.8114127
X-RAY DIFFRACTIONr_lrange_it8.43272.06823552
X-RAY DIFFRACTIONr_lrange_other8.43272.04523540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9751.0511181.232229X-RAY DIFFRACTION99.7874
2.975-3.0561.1371060.9692192X-RAY DIFFRACTION100
3.056-3.1440.744920.7962133X-RAY DIFFRACTION99.8653
3.144-3.2410.6211090.5272061X-RAY DIFFRACTION100
3.241-3.3460.4341190.4192021X-RAY DIFFRACTION100
3.346-3.4630.4341180.3251908X-RAY DIFFRACTION100
3.463-3.5930.4081090.2651868X-RAY DIFFRACTION100
3.593-3.7390.332780.2241814X-RAY DIFFRACTION100
3.739-3.9040.261880.2011730X-RAY DIFFRACTION100
3.904-4.0930.248930.1781660X-RAY DIFFRACTION100
4.093-4.3120.191060.1641575X-RAY DIFFRACTION100
4.312-4.5710.169770.1511512X-RAY DIFFRACTION100
4.571-4.8830.175720.141409X-RAY DIFFRACTION100
4.883-5.2690.207830.1451318X-RAY DIFFRACTION100
5.269-5.7640.201470.171244X-RAY DIFFRACTION100
5.764-6.4320.29440.171140X-RAY DIFFRACTION100
6.432-7.4010.223360.1731002X-RAY DIFFRACTION100
7.401-9.0040.254490.181848X-RAY DIFFRACTION100
9.004-12.4860.219420.194681X-RAY DIFFRACTION100
12.486-44.980.291160.267434X-RAY DIFFRACTION100
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)
10.2375-0.6675-0.24641.93110.48621.2460.04140.00980.0575-0.025-0.047-0.178-0.1105-0.00920.00560.4937-0.0262-0.00830.47560.02740.019873.3003-19.549832.48
20.3435-0.10770.090.4949-0.44110.55350.0248-0.3241-0.16310.3041-0.01590.03140.10160.0788-0.00881.0907-0.02350.01390.80730.09570.089568.3672-21.559786.9014
30.14320.1405-0.03580.325-0.12020.09080.0199-0.25550.01130.26920.01130.01170.0595-0.1461-0.03121.103-0.07680.00421.0233-0.01510.343950.2571-22.11786.5367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA0 - 999
2X-RAY DIFFRACTION2ALLHHH0 - 999
3X-RAY DIFFRACTION3ALLLLL0 - 999

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