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- PDB-6rv6: Structure of properdin lacking TSR3 based on anomalous data -

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Basic information

Entry
Database: PDB / ID: 6rv6
TitleStructure of properdin lacking TSR3 based on anomalous data
Components(Properdin) x 2
KeywordsIMMUNE SYSTEM / innate immunity / complement / protease / regulator
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / positive regulation of immune response ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / positive regulation of immune response / specific granule lumen / tertiary granule lumen / defense response to bacterium / immune response / endoplasmic reticulum lumen / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
: / : / Thrombospondin type 1 repeat / CFP-like, C-terminal thrombospondin type 1 domain / : / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
alpha-D-mannopyranose / Properdin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.507 Å
AuthorsPedersen, D.V. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Citation
Journal: Front Immunol / Year: 2019
Title: Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.
Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / ...Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / Laursen, N.S. / Fremeaux-Bacchi, V. / Andersen, G.R.
#1: Journal: Febs Lett. / Year: 2019
Title: Crystal structure of peptide-bound neprilysin reveals key binding interactions.
Authors: Moss, S. / Subramanian, V. / Acharya, K.R.
#2: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Crystallization and X-ray analysis of monodisperse human properdin.
Authors: Pedersen, D.V. / Revel, M. / Gadeberg, T.A.F. / Andersen, G.R.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / 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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Properdin
B: Properdin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,07218
Polymers43,3612
Non-polymers3,71116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint24 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.790, 219.790, 47.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Properdin / Complement factor P


Mass: 18636.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TB-TSR1-TSR2 and additional residues from expression vector
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / Variant (production host): HEL293F / References: UniProt: P27918
#2: Protein Properdin / Complement factor P


Mass: 24724.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TSR4-5-6 with addiotional residues from expression vector
Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / Variant (production host): HEK293F / References: UniProt: P27918
#3: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 6.61 Å3/Da / Density % sol: 81.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.0 M lithium sulfate, 0.1 M sodium acetate pH 4.0, 0.1 M barium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 2.47968 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.47968 Å / Relative weight: 1
ReflectionResolution: 3.507→155 Å / Num. obs: 27811 / % possible obs: 99.9 % / Redundancy: 20.07 % / Net I/σ(I): 12.2
Reflection shellResolution: 3.507→3.6 Å / Num. unique obs: 2051

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: electron density for TB-TSR1-TSR5-TSR6

Resolution: 3.507→77.707 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.39
RfactorNum. reflection% reflection
Rfree0.2835 1354 4.87 %
Rwork0.2641 --
obs0.2649 27803 99.83 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 3.507→77.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 233 0 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073321
X-RAY DIFFRACTIONf_angle_d1.3844572
X-RAY DIFFRACTIONf_dihedral_angle_d31.651460
X-RAY DIFFRACTIONf_chiral_restr0.071498
X-RAY DIFFRACTIONf_plane_restr0.008559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.507-3.63230.45411180.45142705X-RAY DIFFRACTION99
3.6323-3.77770.451520.34962544X-RAY DIFFRACTION100
3.7777-3.94960.28241330.32462731X-RAY DIFFRACTION100
3.9496-4.15790.25961160.32992599X-RAY DIFFRACTION100
4.1579-4.41830.32491400.27572628X-RAY DIFFRACTION100
4.4183-4.75940.29971480.25362710X-RAY DIFFRACTION100
4.7594-5.23830.31261200.24132642X-RAY DIFFRACTION100
5.2383-5.99610.24811600.25652612X-RAY DIFFRACTION100
5.9961-7.55340.31991440.27272625X-RAY DIFFRACTION100
7.5534-77.72650.22121230.21572653X-RAY DIFFRACTION100

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