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- PDB-6sny: Synthetic mimic of an EPCR-binding PfEMP1 bound to EPCR -

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Basic information

Entry
Database: PDB / ID: 6sny
TitleSynthetic mimic of an EPCR-binding PfEMP1 bound to EPCR
Components
  • Endothelial protein C receptor
  • Synthetic EPCR binding protein
KeywordsIMMUNE SYSTEM / PfEMP1 EPCR vaccine immunogen
Function / homology
Function and homology information


negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space ...negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Endothelial protein C receptor / MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Endothelial protein C receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsBarber, N.M. / Higgins, M.K.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust
Citation
Journal: Msphere / Year: 2021
Title: Structure-Guided Design of a Synthetic Mimic of an Endothelial Protein C Receptor-Binding PfEMP1 Protein.
Authors: Barber, N.M. / Lau, C.K.Y. / Turner, L. / Watson, G. / Thrane, S. / Lusingu, J.P.A. / Lavstsen, T. / Higgins, M.K.
#1: Journal: Biorxiv / Year: 2019
Title: Structure-guided design of a synthetic mimic of an EPCR-binding PfEMP1 protein
Authors: Barber, N.M. / Lau, C.K.Y. / Turner, L. / Watson, G. / Thrane, S. / Luisnghu, J.P.A. / Lavstsen, T. / Higgins, M.K.
History
DepositionAug 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / 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.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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 20, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synthetic EPCR binding protein
B: Endothelial protein C receptor
C: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,10312
Polymers59,5843
Non-polymers4,5199
Water0
1
A: Synthetic EPCR binding protein
B: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8696
Polymers37,5382
Non-polymers2,3324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2346
Polymers22,0471
Non-polymers2,1875
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.729, 112.729, 168.492
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Synthetic EPCR binding protein


Mass: 15491.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Endothelial protein C receptor / / Activated protein C receptor / APC receptor / Endothelial cell protein C receptor


Mass: 22046.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PROCR, EPCR / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9UNN8

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Sugars , 3 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#5: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM

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Details

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: 5.87 Å3/Da / Density % sol: 79.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2M sodium citrate, 0.1M HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→46.88 Å / Num. obs: 20508 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 1 / Rrim(I) all: 0.079 / Net I/σ(I): 1.6
Reflection shellResolution: 3.11→3.19 Å / Num. unique obs: 1635 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→46.88 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.685 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.653 / SU Rfree Blow DPI: 0.355 / SU Rfree Cruickshank DPI: 0.364
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1025 5 %RANDOM
Rwork0.224 ---
obs0.225 20506 89.9 %-
Displacement parametersBiso max: 260.27 Å2 / Biso mean: 128.47 Å2 / Biso min: 67.08 Å2
Baniso -1Baniso -2Baniso -3
1--12.266 Å20 Å20 Å2
2---12.266 Å20 Å2
3---24.532 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 3.11→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 144 0 3858
Biso mean--155.69 --
Num. residues----445
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1575SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes687HARMONIC5
X-RAY DIFFRACTIONt_it3805HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion542SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4467SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d4119HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5571HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion23.13
LS refinement shellResolution: 3.11→3.14 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.378 21 5.11 %
Rwork0.3317 390 -
all-411 -
obs--77.13 %
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)
11.0916-0.3534-1.1319-0.7720.65441.9387-0.0904-0.0286-0.01820.00050.07390.06580.0894-0.38990.01650.0939-0.27330.19060.0584-0.0261-0.057123.256-19.264432.035
20.1292-0.42390.23532.1580.66862.3279-0.06170.29680.12280.0573-0.0542-0.11720.18380.03840.11590.0859-0.08580.0777-0.166-0.0713-0.017643.3799-22.23099.2142
30.72540.3801-0.73780.7992-0.37412.42020.15-0.19940.05020.1806-0.35630.1782-0.10180.17860.2063-0.0406-0.32760.0070.0406-0.119-0.074838.572-45.707-13.7502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 119
2X-RAY DIFFRACTION2{ B|* }B9 - 177
3X-RAY DIFFRACTION3{ C|* }C9 - 177

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