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- PDB-6s8t: Structure of the ICAM-1-binding PfEMP1 IT4var13 DBLbeta domain -

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Basic information

Entry
Database: PDB / ID: 6s8t
TitleStructure of the ICAM-1-binding PfEMP1 IT4var13 DBLbeta domain
ComponentsErythrocyte membrane protein 1
KeywordsPROTEIN BINDING / PfEMP1 / malaria / cytoadhesion / ICAM-1
Function / homology
Function and homology information


host cell surface receptor binding
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 / 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 ...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 / 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
Erythrocyte membrane protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsLennartz, F. / Higgins, M.K.
Funding support1items
OrganizationGrant numberCountry
Wellcome Trust
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural insights into diverse modes of ICAM-1 binding byPlasmodium falciparum-infected erythrocytes.
Authors: Lennartz, F. / Smith, C. / Craig, A.G. / Higgins, M.K.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erythrocyte membrane protein 1


Theoretical massNumber of molelcules
Total (without water)53,8391
Polymers53,8391
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.302, 43.451, 87.129
Angle α, β, γ (deg.)90.000, 103.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Erythrocyte membrane protein 1


Mass: 53839.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: E0A3B3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride hexahydrate 0.1M BIS-Tris pH 5.5 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.17→46.7272 Å / Num. obs: 26322 / % possible obs: 99.81 % / Redundancy: 4.34 % / Net I/σ(I): 5.3
Reflection shellResolution: 2.17→2.21 Å / Num. unique obs: 1229

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→46.7272 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.52
RfactorNum. reflection% reflection
Rfree0.2285 1309 5.01 %
Rwork0.1996 --
obs0.201 26133 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.35 Å2 / Biso mean: 62.4972 Å2 / Biso min: 20.34 Å2
Refinement stepCycle: final / Resolution: 2.17→46.7272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 0 122 3703
Biso mean---48.81 -
Num. residues----442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.17-2.25530.35371300.2981260395
2.2553-2.35790.31371440.2781272999
2.3579-2.48220.31511530.2576272999
2.4822-2.63770.29561690.23582722100
2.6377-2.84140.26621310.23712783100
2.8414-3.12730.24611360.22282798100
3.1273-3.57960.24771400.20032781100
3.5796-4.50940.17771490.1632801100
4.5094-46.7160.19291570.16992878100
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)
15.5958-0.08072.09342.32690.63384.2846-0.07960.0341-0.52890.09330.3009-0.21930.54940.5647-0.13260.37280.0790.04690.3102-0.01030.4768-10.8031-5.0675106.83
23.7022-0.90270.90451.7274-0.60462.8154-0.3745-1.37420.1720.84370.5015-0.0393-0.14380.0763-0.02650.71850.22290.05890.8769-0.08220.3656-20.25647.8395124.3672
35.2056-1.33580.64173.13860.30361.8881-0.0327-0.57230.89170.19210.2904-0.5621-0.19760.67560.10790.38790.06990.03090.5003-0.13890.4088-12.938312.926115.6375
45.0275-0.2327-0.17992.4661-0.21813.1704-0.1804-0.5406-0.25990.26520.3279-0.04580.20720.0819-0.10020.3560.1306-0.00670.33690.02620.2677-15.66850.7667112.8184
54.0893-1.7906-0.69722.75490.2382.2521-0.0551-0.44950.13410.13170.19450.6019-0.3119-0.6367-0.15730.36960.06810.02810.43950.02170.51-41.828417.1788104.757
62.33810.27551.21048.54970.01477.09680.0808-0.16520.3452-0.5899-0.334-0.856-0.17150.59980.12120.36180.05040.09160.27160.02060.3885-14.57979.452389.5943
79.1532-4.9421-3.29736.35912.7424.04260.17650.7131-0.0355-0.2161-0.31990.7385-0.521-1.21740.08770.49650.081-0.09070.57030.03440.5228-39.721811.599494.1132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 733 through 793 )A733 - 793
2X-RAY DIFFRACTION2chain 'A' and (resid 794 through 831 )A794 - 831
3X-RAY DIFFRACTION3chain 'A' and (resid 832 through 870 )A832 - 870
4X-RAY DIFFRACTION4chain 'A' and (resid 871 through 1026 )A871 - 1026
5X-RAY DIFFRACTION5chain 'A' and (resid 1027 through 1106 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1107 through 1136 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1137 through 1202 )A0

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