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- PDB-5mza: The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1 -

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Basic information

Entry
Database: PDB / ID: 5mza
TitleThe DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1
Components
  • Erythrocyte membrane protein 1 (PfEMP1)Red blood cell
  • Intercellular adhesion molecule 1
KeywordsCELL ADHESION / PfEMP1 ICAM-1 Cerebral malaria
Function / homology
Function and homology information


modulation by symbiont of host erythrocyte aggregation / infected host cell surface knob / antigenic variation / regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / adhesion of symbiont to microvasculature / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell ...modulation by symbiont of host erythrocyte aggregation / infected host cell surface knob / antigenic variation / regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / adhesion of symbiont to microvasculature / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / immunological synapse / : / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to leukemia inhibitory factor / cell adhesion molecule binding / cellular response to glucose stimulus / cell-cell adhesion / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / transmembrane signaling receptor activity / integrin binding / virus receptor activity / signaling receptor activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / positive regulation of ERK1 and ERK2 cascade / host cell surface receptor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell adhesion / membrane raft / external side of plasma membrane / focal adhesion / host cell plasma membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / : / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain ...Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment / N-terminal segments of PfEMP1 / Cysteine-rich interdomain region 1 gamma / Cysteine-Rich Interdomain Region 1 gamma / : / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Duffy-binding-like domain / PFEMP1 DBL domain / Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment / acidic terminal segments, variant surface antigen of PfEMP1 / Zn(2)-C6 fungal-type DNA-binding domain / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Intercellular adhesion molecule 1 / Erythrocyte membrane protein 1, PfEMP1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsLennartz, F. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101020/Z/13/Z United Kingdom
CitationJournal: Cell Host Microbe / Year: 2017
Title: Structure-Guided Identification of a Family of Dual Receptor-Binding PfEMP1 that Is Associated with Cerebral Malaria.
Authors: Lennartz, F. / Adams, Y. / Bengtsson, A. / Olsen, R.W. / Turner, L. / Ndam, N.T. / Ecklu-Mensah, G. / Moussiliou, A. / Ofori, M.F. / Gamain, B. / Lusingu, J.P. / Petersen, J.E. / Wang, C.W. ...Authors: Lennartz, F. / Adams, Y. / Bengtsson, A. / Olsen, R.W. / Turner, L. / Ndam, N.T. / Ecklu-Mensah, G. / Moussiliou, A. / Ofori, M.F. / Gamain, B. / Lusingu, J.P. / Petersen, J.E. / Wang, C.W. / Nunes-Silva, S. / Jespersen, J.S. / Lau, C.K. / Theander, T.G. / Lavstsen, T. / Hviid, L. / Higgins, M.K. / Jensen, A.T.
History
DepositionJan 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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.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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 2.1Oct 7, 2020Group: Structure summary / Category: chem_comp / 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: Erythrocyte membrane protein 1 (PfEMP1)
B: Intercellular adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7987
Polymers76,0132
Non-polymers1,7855
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-3 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.639, 109.830, 112.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Erythrocyte membrane protein 1 (PfEMP1) / Red blood cell / Erythrocyte membrane protein 1 / PfEMP1


Mass: 55517.434 Da / Num. of mol.: 1 / Fragment: UNP Residues 728-1214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF11_0521, PF3D7_1150400 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IHM0
#2: Protein Intercellular adhesion molecule 1 / / ICAM-1 / Major group rhinovirus receptor


Mass: 20495.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM1 / Production host: Homo sapiens (human) / References: UniProt: P05362

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Sugars , 2 types, 3 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.: 1 / Source method: obtained synthetically
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
#5: 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: obtained synthetically / 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 , 3 types, 13 molecules

#4: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#6: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 20000, 20% (v/v) PEG 500 and 0.1M Tris-BICINE (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.998 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.78→78.7 Å / Num. obs: 22210 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 59.11 Å2 / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→30.19 Å / Cor.coef. Fo:Fc: 0.9087 / Cor.coef. Fo:Fc free: 0.8776 / SU R Cruickshank DPI: 0.992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.988 / SU Rfree Blow DPI: 0.309 / SU Rfree Cruickshank DPI: 0.314
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 1103 5.01 %RANDOM
Rwork0.2048 ---
obs0.2063 22036 99.74 %-
Displacement parametersBiso mean: 47.66 Å2
Baniso -1Baniso -2Baniso -3
1-6.3974 Å20 Å20 Å2
2---2.4642 Å20 Å2
3----3.9333 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.78→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 105 11 5086
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075207HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.977079HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1849SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes146HARMONIC2
X-RAY DIFFRACTIONt_gen_planes730HARMONIC5
X-RAY DIFFRACTIONt_it5207HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion17.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion665SEMIHARMONIC5
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_contact5673SEMIHARMONIC4
LS refinement shellResolution: 2.78→2.92 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2828 141 4.87 %
Rwork0.2313 2753 -
all0.2338 2894 -
obs--99.74 %
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)
11.2151-0.083-0.1740.99410.19381.29070.035-0.151-0.01940.0975-0.04620.02150.12350.060.0112-0.1057-0.04580.0061-0.1111-0.0084-0.0904-8.8518-9.315146.1861
20.54991.1073-0.96543.025-3.0545.0161-0.16770.1142-0.0508-0.18220.06410.06220.5984-0.11380.1036-0.06960.01380.0456-0.1121-0.0028-0.07964.3137-20.69779.7173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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