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- PDB-4v3d: The CIDRa domain from HB3var03 PfEMP1 bound to endothelial protei... -

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Basic information

Entry
Database: PDB / ID: 4v3d
TitleThe CIDRa domain from HB3var03 PfEMP1 bound to endothelial protein C receptor
Components
  • ENDOTHELIAL PROTEIN C RECEPTOR
  • HB3VAR03 CIDRA DOMAIN
KeywordsSIGNALING PROTEIN / PFEMP1 / EPCR / MALARIA / CIDR DOMAIN / ENDOTHELIAL PROTEIN C RECEPTOR
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 speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLau, C.K.Y. / Turner, L. / Jespersen, J.S. / Lowe, E.D. / Petersen, B. / Wang, C.W. / Petersen, J.E.V. / Lusingu, J. / Theander, T.G. / Lavstsen, T. / Higgins, M.K.
CitationJournal: Cell Host Microbe. / Year: 2015
Title: Structural Conservation Despite Huge Sequence Diversity Allows Epcr Binding by the Pfemp1 Family Implicated in Severe Childhood Malaria.
Authors: Lau, C.K.Y. / Turner, L. / Jespersen, J.S. / Lowe, E.D. / Petersen, B. / Wang, C.W. / Petersen, J.E.V. / Lusingu, J. / Theander, T.G. / Lavstsen, T. / Higgins, M.K.
History
DepositionOct 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_label_seq_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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HB3VAR03 CIDRA DOMAIN
B: ENDOTHELIAL PROTEIN C RECEPTOR
C: HB3VAR03 CIDRA DOMAIN
D: ENDOTHELIAL PROTEIN C RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,88914
Polymers98,3114
Non-polymers4,57810
Water00
1
C: HB3VAR03 CIDRA DOMAIN
D: ENDOTHELIAL PROTEIN C RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5467
Polymers49,1552
Non-polymers2,3915
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-3.1 kcal/mol
Surface area19510 Å2
MethodPISA
2
A: HB3VAR03 CIDRA DOMAIN
B: ENDOTHELIAL PROTEIN C RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3437
Polymers49,1552
Non-polymers2,1875
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-3.6 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.130, 94.670, 290.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HB3VAR03 CIDRA DOMAIN


Mass: 29457.137 Da / Num. of mol.: 2 / Fragment: CIDRA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: HB3 / Plasmid: PET15B / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834
#2: Protein ENDOTHELIAL PROTEIN C RECEPTOR


Mass: 19698.246 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 468-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEXPRES2-1 / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q9UNN8

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Sugars , 3 types, 8 molecules

#3: 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.: 3
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
#4: 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.: 2
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
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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


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

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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: 2.31 Å3/Da / Density % sol: 46.85 % / Description: NONE
Crystal growpH: 8 / Details: 0.2 M NANO3, 0.1 M BTP PH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: PILATUS / Detector: PIXEL / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→53.29 Å / Num. obs: 25427 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 68.37 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L8J

1l8j


Resolution: 2.65→53.29 Å / Cor.coef. Fo:Fc: 0.9141 / Cor.coef. Fo:Fc free: 0.9013 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.175 / SU Rfree Blow DPI: 0.337
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 1287 5.06 %RANDOM
Rwork0.2224 ---
obs0.2241 25427 94.01 %-
Displacement parametersBiso mean: 66.61 Å2
Baniso -1Baniso -2Baniso -3
1--7.3732 Å20 Å20 Å2
2---3.8568 Å20 Å2
3---11.2299 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.65→53.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6093 0 304 0 6397
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096563HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.258874HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2417SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes196HARMONIC2
X-RAY DIFFRACTIONt_gen_planes899HARMONIC5
X-RAY DIFFRACTIONt_it6563HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion21.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion871SEMIHARMONIC5
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_contact7059SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.76 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3069 123 4.29 %
Rwork0.2636 2747 -
all0.2655 2870 -
obs--94.01 %
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)
10.8562-0.72480.32843.714-0.01142.1042-0.0046-0.06980.06130.09150.10620.3595-0.0946-0.3553-0.1017-0.15830.0319-0.0066-0.1158-0.023-0.0034-14.2345-19.313-62.4539
22.49930.320.58931.51260.0434.70140.0352-0.37690.0410.2776-0.0136-0.22470.14440.1327-0.0216-0.04020.0379-0.0617-0.1068-0.0024-0.11362.931-41.6151-49.6384
33.3233-0.80390.56362.31350.49873.8036-0.2702-0.07290.4233-0.20730.10910.38-0.5442-0.21070.1611-0.1630.0019-0.152-0.16150.0426-0.1102-35.6892-35.1317-13.0446
42.65150.2108-1.39082.73340.47595.5289-0.2570.0309-0.1737-0.44530.2682-0.03130.5317-0.0208-0.0112-0.0469-0.152-0.0078-0.03290.0792-0.2624-15.3044-54.3663-22.3874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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