[English] 日本語
Yorodumi
- PDB-6ss4: Structure of arginase-2 in complex with the inhibitory human anti... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
: / 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more