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- PDB-6ss6: Structure of arginase-2 in complex with the inhibitory human anti... -

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Basic information

Entry
Database: PDB / ID: 6ss6
TitleStructure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0020187
Components
  • Arginase-2, mitochondrial
  • Fab C0020187 heavy chain (IgG1)
  • Fab C0020187 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 / arginase ...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 / arginase / arginase activity / : / urea cycle / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-17 production / ureteric bud development / regulation of reactive oxygen species biosynthetic process / negative regulation of tumor necrosis factor production / striated muscle contraction / nitric oxide biosynthetic process / Mitochondrial protein degradation / 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
: / Arginase-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Extensive sequence and structural evolution of Arginase 2 inhibitory antibodies enabled by an unbiased approach to affinity maturation.
Authors: Chan, D.T.Y. / Jenkinson, L. / Haynes, S.W. / Austin, M. / Diamandakis, A. / Burschowsky, D. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / ...Authors: Chan, D.T.Y. / Jenkinson, L. / Haynes, S.W. / Austin, M. / Diamandakis, A. / Burschowsky, D. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / Gowans, E. / Shibata, Y. / Barnard, 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 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 5, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Jan 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Arginase-2, mitochondrial
BBB: Arginase-2, mitochondrial
CCC: Arginase-2, mitochondrial
HHH: Fab C0020187 heavy chain (IgG1)
III: Fab C0020187 heavy chain (IgG1)
JJJ: Fab C0020187 heavy chain (IgG1)
LLL: Fab C0020187 light chain (IgG1)
MMM: Fab C0020187 light chain (IgG1)
NNN: Fab C0020187 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,98142
Polymers256,0589
Non-polymers2,92333
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24740 Å2
ΔGint-424 kcal/mol
Surface area92300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.126, 138.126, 551.307
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains B C
44Chains H I
55Chains H J
66Chains I J
77Chains L M
88Chains L N
99Chains M N

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

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


Mass: 37808.594 Da / Num. of mol.: 3
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 C0020187 heavy chain (IgG1)


Mass: 24479.453 Da / Num. of mol.: 3
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 C0020187 light chain (IgG1)


Mass: 23064.469 Da / Num. of mol.: 3
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.: 6 / Source method: obtained synthetically / Formula: Mn
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.25→48.78 Å / Num. obs: 50453 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.78 / Net I/σ(I): 4.2
Reflection shellResolution: 3.25→3.36 Å / Redundancy: 9.9 % / Rmerge(I) obs: 8.48 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4555 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZE,6SS5

4hze

6ss5


Resolution: 3.25→48.755 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.825 / SU B: 66.427 / SU ML: 0.949 / Cross valid method: FREE R-VALUE / ESU R Free: 0.711
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3606 2549 5.066 %
Rwork0.3003 --
all0.303 --
obs-50320 99.901 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 99.097 Å2
Baniso -1Baniso -2Baniso -3
1--4.897 Å2-2.448 Å20 Å2
2---4.897 Å20 Å2
3---15.886 Å2
Refinement stepCycle: LAST / Resolution: 3.25→48.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16814 0 141 0 16955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01317342
X-RAY DIFFRACTIONr_bond_other_d0.0020.01715678
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.63723611
X-RAY DIFFRACTIONr_angle_other_deg1.171.56936533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72352234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81122.544735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.106152706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7071581
X-RAY DIFFRACTIONr_chiral_restr0.060.22291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219344
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023425
X-RAY DIFFRACTIONr_nbd_refined0.2230.24076
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.216777
X-RAY DIFFRACTIONr_nbtor_refined0.1630.28271
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.29039
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2526
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3120.278
X-RAY DIFFRACTIONr_nbd_other0.3150.2258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3180.215
X-RAY DIFFRACTIONr_mcbond_it4.60210.7878963
X-RAY DIFFRACTIONr_mcbond_other4.60110.7878962
X-RAY DIFFRACTIONr_mcangle_it7.8216.1711188
X-RAY DIFFRACTIONr_mcangle_other7.8216.1711189
X-RAY DIFFRACTIONr_scbond_it3.67510.8998376
X-RAY DIFFRACTIONr_scbond_other3.67310.8428269
X-RAY DIFFRACTIONr_scangle_it6.50716.30912423
X-RAY DIFFRACTIONr_scangle_other6.51916.22412262
X-RAY DIFFRACTIONr_lrange_it15.185201.76570418
X-RAY DIFFRACTIONr_lrange_other15.185201.76570419
X-RAY DIFFRACTIONr_ncsr_local_group_10.1660.059303
X-RAY DIFFRACTIONr_ncsr_local_group_20.1860.059279
X-RAY DIFFRACTIONr_ncsr_local_group_30.1810.059154
X-RAY DIFFRACTIONr_ncsr_local_group_40.1730.056038
X-RAY DIFFRACTIONr_ncsr_local_group_50.1930.055779
X-RAY DIFFRACTIONr_ncsr_local_group_60.1890.055693
X-RAY DIFFRACTIONr_ncsr_local_group_70.1460.055875
X-RAY DIFFRACTIONr_ncsr_local_group_80.2250.055275
X-RAY DIFFRACTIONr_ncsr_local_group_90.2260.055291
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
3.25-3.3340.4621640.45334630.45336290.430.45799.94490.459
3.334-3.4250.4531790.42533640.42635430.4820.5121000.428
3.425-3.5240.3711490.4232840.41834330.3840.3471000.42
3.524-3.6320.4321610.431980.40133590.4190.4681000.397
3.632-3.750.421520.36230850.36532370.5510.5651000.355
3.75-3.8810.3661570.33729750.33931320.6280.6561000.326
3.881-4.0260.3651610.30628870.30930490.6830.70399.96720.291
4.026-4.190.3291500.28728070.28929570.7120.7631000.268
4.19-4.3740.3141350.25626750.25828100.8320.8571000.235
4.374-4.5860.3051480.23625680.2427160.8640.881000.211
4.586-4.8320.2581440.23524370.23725820.8980.89899.96130.208
4.832-5.1220.3111320.24523330.24924650.8670.8911000.217
5.122-5.4710.3031240.27222100.27423340.8710.8731000.242
5.471-5.9030.3951200.27620490.28321690.820.8661000.246
5.903-6.4570.4011230.26419060.27320290.8420.8771000.232
6.457-7.2030.325970.25717570.26118540.8740.881000.228
7.203-8.2880.35670.23815830.24216500.8660.9051000.218
8.288-10.0780.348840.24513630.25114470.8850.9351000.238
10.078-13.9570.355590.27411080.27811670.890.9321000.268
13.957-48.7550.526430.4237190.4297620.8420.8641000.399

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