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- PDB-6lyc: Crystal structure of the NOD SIRPa complex with D4-2 -

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Entry
Database: PDB / ID: 6lyc
TitleCrystal structure of the NOD SIRPa complex with D4-2
Components
  • D4-2
  • SIRPa of the NOD mouse strain
KeywordsCELL ADHESION / complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsMurata, Y. / Matsuda, M. / Nakagawa, A. / Matozaki, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H04032 Japan
Japan Agency for Medical Research and Development (AMED)18cm0106308h003 Japan
Japan Agency for Medical Research and Development (AMED)19cm0106308h004 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101072 (support number 1143) Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072 Japan
CitationJournal: Cell Chem Biol / Year: 2020
Title: Macrocyclic Peptide-Mediated Blockade of the CD47-SIRP alpha Interaction as a Potential Cancer Immunotherapy.
Authors: Hazama, D. / Yin, Y. / Murata, Y. / Matsuda, M. / Okamoto, T. / Tanaka, D. / Terasaka, N. / Zhao, J. / Sakamoto, M. / Kakuchi, Y. / Saito, Y. / Kotani, T. / Nishimura, Y. / Nakagawa, A. / Suga, H. / Matozaki, T.
History
DepositionFeb 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / software / struct_conn
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / refine / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine.details / _refine.ls_R_factor_R_free_error / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.percent_reflns_R_free / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_chi_squared / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIRPa of the NOD mouse strain
B: D4-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2313
Polymers15,1712
Non-polymers601
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-9 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.967, 30.721, 43.482
Angle α, β, γ (deg.)90.00, 100.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody SIRPa of the NOD mouse strain


Mass: 13355.909 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide D4-2


Mass: 1815.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.8 Å3/Da / Density % sol: 31.67 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M imidazole, 0.1 M MES (pH 6.5), 0.09 M NaF, 0.09 M NaBr, 0.09 M NaI, 12.5% MPD (2-Methyl-2,4-pentanediol), 12.5% PEG1000, and 12.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2018
Details: Double Mirrors, Si(111) double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.36→40.82 Å / Num. obs: 22244 / % possible obs: 95.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.66 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.4
Reflection shellResolution: 1.36→1.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.393 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
autoPROCsnapshot_20181127data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YZ1

2yz1


Resolution: 1.36→28.75 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.13
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1068 4.82 %random
Rwork0.204 ---
obs0.204 22158 94.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 1.36→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 7 70 1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011074
X-RAY DIFFRACTIONf_angle_d1.1191473
X-RAY DIFFRACTIONf_dihedral_angle_d19.3395
X-RAY DIFFRACTIONf_chiral_restr0.1168
X-RAY DIFFRACTIONf_plane_restr0.009189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.420.33291310.31222653X-RAY DIFFRACTION96
1.42-1.50.30341190.2852659X-RAY DIFFRACTION97
1.5-1.590.30051480.26292647X-RAY DIFFRACTION96
1.59-1.720.29151230.26492654X-RAY DIFFRACTION95
1.72-1.890.28951320.24972547X-RAY DIFFRACTION92
1.89-2.160.23451350.21682528X-RAY DIFFRACTION92
2.16-2.720.22911330.22082697X-RAY DIFFRACTION96
2.72-28.750.18451470.17472705X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 11.9643 Å / Origin y: -13.3855 Å / Origin z: -10.7054 Å
111213212223313233
T0.1817 Å20.0032 Å20.0066 Å2-0.2229 Å20.0622 Å2--0.2794 Å2
L3.0711 °2-0.6565 °20.1787 °2-2.8527 °21.178 °2--3.6714 °2
S-0.0624 Å °-0.1153 Å °-0.047 Å °0.0055 Å °0.1102 Å °-0.014 Å °0.058 Å °0.1977 Å °-0.0334 Å °
Refinement TLS groupSelection details: ALL

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