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- PDB-4k2u: Crystal structure of PfEBA-175 F1 in complex with R218 antibody F... -

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Basic information

Entry
Database: PDB / ID: 4k2u
TitleCrystal structure of PfEBA-175 F1 in complex with R218 antibody Fab fragment
Components
  • Antibody Heavy Chain
  • Antibody Light Chain
  • Erythrocyte binding antigen 175
KeywordsIMMUNE SYSTEM / DBL domain / Immunoglobulin domain / Antibody fragment / Cell attachment / Immunity / Receptor / Ligand / Extracellular
Function / homology
Function and homology information


microneme / symbiont entry into host / heparin binding / host cell surface receptor binding / membrane
Similarity search - Function
Erythrocyte binding antigen 175, C-terminal / Erythrocyte binding antigen 175, C-terminal domain superfamily / Erythrocyte binding antigen 175 / Duffy-antigen binding / Duffy-antigen binding superfamily / Duffy binding domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Erythrocyte binding antigen-175
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTolia, N.H.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural and Functional Basis for Inhibition of Erythrocyte Invasion by Antibodies that Target Plasmodium falciparum EBA-175.
Authors: Chen, E. / Paing, M.M. / Salinas, N. / Sim, B.K. / Tolia, N.H.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erythrocyte binding antigen 175
B: Erythrocyte binding antigen 175
H: Antibody Heavy Chain
I: Antibody Heavy Chain
L: Antibody Light Chain
M: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,04518
Polymers172,8936
Non-polymers1,15312
Water3,081171
1
A: Erythrocyte binding antigen 175
H: Antibody Heavy Chain
L: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,11910
Polymers86,4463
Non-polymers6727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Erythrocyte binding antigen 175
I: Antibody Heavy Chain
M: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9278
Polymers86,4463
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.950, 53.530, 156.790
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Erythrocyte binding antigen 175


Mass: 35274.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: eba-175, MAL7P1.176 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IBE8
#2: Antibody Antibody Heavy Chain


Mass: 25216.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Antibody Light Chain


Mass: 25955.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M phosphate-citrate, 0.4 M lithium sulfate, 30% PEG 1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791212 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791212 Å / Relative weight: 1
ReflectionResolution: 2.4→29.793 Å / Num. obs: 66216 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→29.793 Å / SU ML: 0.31 / σ(F): 2 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1994 3.19 %
Rwork0.2041 --
obs0.2057 62598 99.44 %
all-66216 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→29.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10543 0 60 171 10774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210848
X-RAY DIFFRACTIONf_angle_d0.60914646
X-RAY DIFFRACTIONf_dihedral_angle_d11.7173961
X-RAY DIFFRACTIONf_chiral_restr0.0391578
X-RAY DIFFRACTIONf_plane_restr0.0021838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.51130.33611330.27884273X-RAY DIFFRACTION100
2.5113-2.57910.3341480.26324292X-RAY DIFFRACTION100
2.5791-2.6550.32541410.25384284X-RAY DIFFRACTION99
2.655-2.74060.29731440.24754296X-RAY DIFFRACTION100
2.7406-2.83850.32841400.24234334X-RAY DIFFRACTION100
2.8385-2.9520.33461420.23134337X-RAY DIFFRACTION100
2.952-3.08620.28321380.2434290X-RAY DIFFRACTION100
3.0862-3.24880.30771460.23474323X-RAY DIFFRACTION100
3.2488-3.4520.30351490.22954343X-RAY DIFFRACTION100
3.452-3.71810.2481390.20974347X-RAY DIFFRACTION100
3.7181-4.09140.26491380.18524379X-RAY DIFFRACTION100
4.0914-4.68150.18731440.15984357X-RAY DIFFRACTION100
4.6815-5.89070.19951470.16694419X-RAY DIFFRACTION100
5.8907-29.79550.23551450.20914330X-RAY DIFFRACTION95
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)
12.4540.24040.58351.334-0.1966.7704-0.1291-0.0040.1794-0.02750.0652-0.1228-0.1520.45510.08560.2872-0.0253-0.00750.40810.02030.4725-72.410565.8693-240.3809
24.8581-1.7081-2.6164.2061.15043.9001-0.02140.03790.02130.11650.1927-0.30260.09490.3304-0.15050.33950.0327-0.02160.6212-0.13020.4319-39.380476.8254-207.058
31.56011.39610.39182.72851.21141.65630.03960.07290.0140.026-0.0514-0.0104-0.0753-0.0021-0.01960.20630.21280.01050.31960.07260.234-69.569671.8006-195.7141
41.44490.8253-0.42662.57350.8321.56040.1941-0.3884-0.07590.6715-0.2338-0.07590.26280.01850.09630.42410.3513-0.10960.65650.29970.2923-83.085471.3071-163.5929
50.23990.76480.34141.04520.90180.71770.11-0.02110.09470.1606-0.09280.1843-0.0227-0.1372-0.02620.4830.14530.00140.4442-0.01490.4907-79.704372.7849-191.7568
60.54060.82840.06742.02940.84080.88210.0406-0.18230.17540.0801-0.21020.437-0.0766-0.12720.15290.62370.14970.05950.80370.0060.6815-87.971675.0809-165.3676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 9:283 )B9 - 283
2X-RAY DIFFRACTION2( CHAIN A AND RESID 10:281 )A10 - 281
3X-RAY DIFFRACTION3( CHAIN M AND RESID 1:108 ) OR ( CHAIN L AND RESID 1:108 )M1 - 108
4X-RAY DIFFRACTION3( CHAIN M AND RESID 1:108 ) OR ( CHAIN L AND RESID 1:108 )L1 - 108
5X-RAY DIFFRACTION4( CHAIN M AND RESID 109:200 ) OR ( CHAIN L AND RESID 109:210 )M109 - 200
6X-RAY DIFFRACTION4( CHAIN M AND RESID 109:200 ) OR ( CHAIN L AND RESID 109:210 )L109 - 210
7X-RAY DIFFRACTION5( CHAIN I AND RESID 1:114 ) OR ( CHAIN H AND RESID 1:114 )I1 - 114
8X-RAY DIFFRACTION5( CHAIN I AND RESID 1:114 ) OR ( CHAIN H AND RESID 1:114 )H1 - 114
9X-RAY DIFFRACTION6( CHAIN I AND RESID 115:212 ) OR ( CHAIN H AND RESID 115:212 )I115 - 212
10X-RAY DIFFRACTION6( CHAIN I AND RESID 115:212 ) OR ( CHAIN H AND RESID 115:212 )H115 - 212

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