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- PDB-5lgd: The CIDRa domain from MCvar1 PfEMP1 bound to CD36 -

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Basic information

Entry
Database: PDB / ID: 5lgd
TitleThe CIDRa domain from MCvar1 PfEMP1 bound to CD36
Components
  • PfEMP1 variant 1 of strain MC
  • Platelet glycoprotein 4
KeywordsCELL ADHESION / Plasmodium falciparum cytoadhesion scavenger receptor malaria
Function / homology
Function and homology information


short-chain fatty acid transmembrane transporter activity / short-chain fatty acid transport / lipoteichoic acid immune receptor activity / oxidised low-density lipoprotein particle clearance / oxidised low-density lipoprotein particle receptor activity / Intracellular metabolism of fatty acids regulates insulin secretion / oleate transmembrane transporter activity / long-chain fatty acid import across plasma membrane / response to linoleic acid / Toll Like Receptor TLR6:TLR2 Cascade ...short-chain fatty acid transmembrane transporter activity / short-chain fatty acid transport / lipoteichoic acid immune receptor activity / oxidised low-density lipoprotein particle clearance / oxidised low-density lipoprotein particle receptor activity / Intracellular metabolism of fatty acids regulates insulin secretion / oleate transmembrane transporter activity / long-chain fatty acid import across plasma membrane / response to linoleic acid / Toll Like Receptor TLR6:TLR2 Cascade / low-density lipoprotein particle mediated signaling / cellular response to diacyl bacterial lipopeptide / regulation of action potential / triglyceride transport / long-chain fatty acid import into cell / response to stilbenoid / production of molecular mediator involved in inflammatory response / positive regulation of cholesterol storage / lipid transport across blood-brain barrier / plasma lipoprotein particle clearance / positive regulation of blood microparticle formation / Scavenging by Class B Receptors / regulation of lipopolysaccharide-mediated signaling pathway / cholesterol import / cellular response to hydroperoxide / low-density lipoprotein particle clearance / high-density lipoprotein particle binding / intestinal cholesterol absorption / cellular response to oxidised low-density lipoprotein particle stimulus / Toll-like receptor binding / regulation of removal of superoxide radicals / Cross-presentation of particulate exogenous antigens (phagosomes) / low-density lipoprotein particle receptor activity / low-density lipoprotein particle binding / phagocytosis, recognition / amyloid-beta clearance by cellular catabolic process / response to fatty acid / positive regulation of phagocytosis, engulfment / Regulation of TLR by endogenous ligand / platelet alpha granule membrane / lipid storage / cholesterol transport / transforming growth factor beta binding / MyD88 deficiency (TLR2/4) / positive regulation of macrophage derived foam cell differentiation / intestinal absorption / apoptotic cell clearance / cargo receptor activity / IRAK4 deficiency (TLR2/4) / long-chain fatty acid transmembrane transporter activity / positive regulation of macrophage cytokine production / cGMP-mediated signaling / lipoprotein transport / scavenger receptor activity / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of cell-matrix adhesion / phagocytosis, engulfment / negative regulation of protein import into nucleus / regulation of toll-like receptor signaling pathway / response to lipid / thrombospondin receptor activity / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / cellular response to lipoteichoic acid / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / positive regulation of blood coagulation / regulation of protein-containing complex assembly / long-chain fatty acid transport / fatty acid transport / specific granule membrane / nitric oxide-cGMP-mediated signaling / energy homeostasis / phagocytic vesicle / positive regulation of interleukin-12 production / receptor-mediated endocytosis / negative regulation of angiogenesis / positive regulation of interleukin-1 beta production / fatty acid metabolic process / cell periphery / brush border membrane / PPARA activates gene expression / caveola / receptor internalization / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / positive regulation of interleukin-6 production / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / blood coagulation / positive regulation of nitric oxide biosynthetic process / endocytic vesicle membrane / MAPK cascade / Platelet degranulation / sensory perception of taste / amyloid-beta binding / positive regulation of cold-induced thermogenesis / ER-Phagosome pathway / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis
Similarity search - Function
CD36/scavenger receptor class B member 1 / CD36 family / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / CD36 family / N-terminal segments of PfEMP1 / : / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain ...CD36/scavenger receptor class B member 1 / CD36 family / Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / CD36 family / N-terminal segments of PfEMP1 / : / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / Duffy-binding-like domain, C-terminal subdomain / Duffy-binding-like domain / PFEMP1 DBL domain / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment superfamily / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / acidic terminal segments, variant surface antigen of PfEMP1 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain
Similarity search - Domain/homology
PALMITIC ACID / Platelet glycoprotein 4 / PfEMP1 variant 1 of strain MC
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsHsieh, F.L. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101020/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: The structural basis for CD36 binding by the malaria parasite.
Authors: Hsieh, F.L. / Turner, L. / Bolla, J.R. / Robinson, C.V. / Lavstsen, T. / Higgins, M.K.
History
DepositionJul 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
Revision 2.2Nov 6, 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: Platelet glycoprotein 4
B: PfEMP1 variant 1 of strain MC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,59420
Polymers74,0202
Non-polymers3,57418
Water2,738152
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint41 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.826, 40.726, 138.836
Angle α, β, γ (deg.)90.00, 114.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Platelet glycoprotein 4 / Fatty acid translocase / FAT / Glycoprotein IIIb / GPIIIB / Leukocyte differentiation antigen CD36 ...Fatty acid translocase / FAT / Glycoprotein IIIb / GPIIIB / Leukocyte differentiation antigen CD36 / PAS IV / PAS-4 / Platelet collagen receptor / Platelet glycoprotein IV / GPIV / Thrombospondin receptor


Mass: 53104.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD36, GP3B, GP4 / Production host: Homo sapiens (human) / References: UniProt: P16671
#2: Protein PfEMP1 variant 1 of strain MC


Mass: 20915.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: MCvar-1 PfEMP1 / Production host: Homo sapiens (human) / References: UniProt: Q25733

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Sugars , 2 types, 9 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.: 1
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: 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.: 8
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 , 4 types, 161 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 20% (w/v) PEG6000, 0.1 M Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.07→63 Å / Num. obs: 40626 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.48 Å2 / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7B

4f7b


Resolution: 2.07→62.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.209 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 2057 5.08 %RANDOM
Rwork0.2124 ---
obs0.2145 40526 99.25 %-
Displacement parametersBiso mean: 48.28 Å2
Baniso -1Baniso -2Baniso -3
1-3.7116 Å20 Å27.1913 Å2
2---2.3634 Å20 Å2
3----1.3482 Å2
Refine analyzeLuzzati coordinate error obs: 0.374 Å
Refinement stepCycle: 1 / Resolution: 2.07→62.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 233 152 4875
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014835HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.196546HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1765SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes130HARMONIC2
X-RAY DIFFRACTIONt_gen_planes673HARMONIC5
X-RAY DIFFRACTIONt_it4835HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion20.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion655SEMIHARMONIC5
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_contact5659SEMIHARMONIC4
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3099 127 4.27 %
Rwork0.2781 2847 -
all0.2794 2974 -
obs--99.25 %
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)
11.3651-0.47741.01370.5309-0.38852.96080.04070.27990.0978-0.1161-0.1293-0.1268-0.10320.14250.0886-0.0753-0.0046-0.0206-0.0657-0.00960.0157-41.7774-27.449525.0785
20.94680.02891.21230.5021-0.2915.4330.1706-0.5822-0.20850.0086-0.02510.05270.425-0.9102-0.1455-0.2373-0.1073-0.04610.23050.07390.0188-49.1411-40.615176.2292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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