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- PDB-5ezo: Crystal Structure of PfCyRPA in complex with an invasion-inhibito... -

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Basic information

Entry
Database: PDB / ID: 5ezo
TitleCrystal Structure of PfCyRPA in complex with an invasion-inhibitory antibody Fab.
Components
  • PfCyRPA
  • c12 FAB
  • c12 Fab
KeywordsIMMUNE SYSTEM / MALARIA INHIBITORY ANTIBODY / FAB / cyrpa
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / apical part of cell / cytoplasmic vesicle / host extracellular space / host cell plasma membrane / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
Cysteine-rich protective antigen 6 bladed domain / Cysteine-Rich Protective Antigen 6 bladed domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cysteine-rich protective antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.63 Å
AuthorsFavuzza, P. / Pluschke, G. / Rudolph, M.G.
CitationJournal: Elife / Year: 2017
Title: Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody.
Authors: Favuzza, P. / Guffart, E. / Tamborrini, M. / Scherer, B. / Dreyer, A.M. / Rufer, A.C. / Erny, J. / Hoernschemeyer, J. / Thoma, R. / Schmid, G. / Gsell, B. / Lamelas, A. / Benz, J. / Joseph, ...Authors: Favuzza, P. / Guffart, E. / Tamborrini, M. / Scherer, B. / Dreyer, A.M. / Rufer, A.C. / Erny, J. / Hoernschemeyer, J. / Thoma, R. / Schmid, G. / Gsell, B. / Lamelas, A. / Benz, J. / Joseph, C. / Matile, H. / Pluschke, G. / Rudolph, M.G.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Structure summary
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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 / _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.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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 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
H: PfCyRPA
L: c12 FAB
A: c12 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1444
Polymers86,5743
Non-polymers5711
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-13 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.801, 44.681, 121.336
Angle α, β, γ (deg.)90.000, 108.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody PfCyRPA / heavy chain


Mass: 23676.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody c12 FAB / Fab light chain


Mass: 23581.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody c12 Fab


Mass: 39316.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PFD1130w / Production host: Mus musculus (house mouse) / References: UniProt: Q8IFM8
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium citrate pH 5.5, 17 % PEG 5000 MME, 0.2 M NDSB-201

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.63→43 Å / Num. obs: 11401 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 60.184 Å2 / CC1/2: 0.921 / Rmerge(I) obs: 0.497 / Rrim(I) all: 0.595 / Χ2: 0.759 / Net I/σ(I): 2.63 / Num. measured all: 37178
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.63-3.723.32.6730.427738668550.353.18198.7
3.72-3.832.0260.5426977867840.3342.40499.7
3.83-3.941.3910.826998017970.421.65799.5
3.94-4.061.1840.9325927827640.5741.40997.7
4.06-4.191.0371.1124657337290.6611.23599.5
4.19-4.340.6071.8123727207170.8740.72799.6
4.34-4.50.5661.8822067117030.8530.68598.9
4.5-4.690.4652.3721186636580.8470.55999.2
4.69-4.890.422.5720346506500.8640.504100
4.89-5.130.3752.9220596136110.8970.44799.7
5.13-5.410.4362.6519945935890.8680.52199.3
5.41-5.740.422.6118385615540.8680.50198.8
5.74-6.140.4332.517455345310.8610.5299.4
6.14-6.630.4842.2815245054980.8070.58798.6
6.63-7.260.3862.8514344624630.8480.467100
7.26-8.120.244.3113474244190.960.28698.8
8.12-9.370.131711863673660.9860.15999.7
9.37-11.480.08110.569583123130.9940.098100
11.48-16.230.07211.57262622570.9920.08898.1
16.230.04414.354111541430.9980.05492.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ezi, 5ezn

5ezi

5ezn


Resolution: 3.63→43 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.33 544 4.79 %
Rwork0.2737 --
obs0.2763 11357 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.29 Å2 / Biso mean: 70.7961 Å2 / Biso min: 33.49 Å2
Refinement stepCycle: final / Resolution: 3.63→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 38 0 6033
Biso mean--112.4 --
Num. residues----756
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)
13.3728-0.30621.05282.0228-0.2171.8463-0.1470.884-0.424-0.42390.0126-0.3447-0.25850.18220.18140.66430.01040.06080.7059-0.27730.58093.40710.2549-35.4266
23.29640.37210.31040.11631.35881.5089-0.07642.0231-0.0352-0.0795-0.0190.2525-0.10240.32550.04140.8716-0.1033-0.03671.2709-0.1390.515-25.09963.3185-46.9995
32.32061.0654-0.98311.2088-1.02361.57620.07570.39290.00240.00310.0599-0.0742-0.4840.19790.12260.65130.1614-0.12730.28830.05790.4015-8.837211.3398-19.3945
42.7955-0.5595-1.74092.63370.13884.7328-0.10980.8279-0.34260.07850.2050.44860.1559-1.7495-0.13280.6392-0.15940.03271.334-0.23420.7412-38.8333-0.4642-37.9811
51.56950.20312.42442.07260.56052.73860.11430.2846-0.32860.02180.19850.33150.25510.83150.0560.393-0.01530.05520.4249-0.02730.795615.492825.5493-2.3849
64.32490.8277-0.77521.54051.62194.7879-0.29460.1467-0.1484-0.4315-0.02880.0940.21480.57420.11490.42050.1123-0.00580.63990.06440.577217.034516.4869-16.4872
78.5864-1.6511-2.67156.88411.91783.94070.23421.8335-0.757-0.0771-0.43650.46220.1110.25490.16730.73610.16650.00050.9318-0.08580.488724.120217.1683-25.3699
82.92132.179-2.045.87031.45763.6742-0.66130.4890.0981-0.1180.9914-0.6528-0.09041.4874-0.0630.4573-0.149-0.13131.36530.22710.738835.589923.1998-18.9444
93.92121.2835-2.08451.03490.02872.12290.6183-1.2859-0.93281.6671-1.3029-1.07352.39281.4573-0.18141.23760.5245-0.51270.92950.17410.65445.88514.8585-11.7121
103.55430.2924-0.48021.67880.48944.2299-0.69670.1748-0.9385-0.1660.5827-0.83840.3320.52920.08440.6254-0.06090.01660.78-0.09520.825838.788921.9069-12.9392
117.28680.3304-1.35622.7945-0.12686.4645-0.15470.4986-0.50780.12280.3395-0.7393-0.07520.0847-0.24790.5366-0.1259-0.06640.5373-0.12150.75133.61224.00642.6604
120.5596-0.74190.26331.24930.71614.9770.19670.2668-0.24410.330.7698-0.29371.1508-0.79560.46280.2650.5143-0.46060.45430.0111.394614.986612.79899.5571
134.474-1.4116-0.22724.70811.62915.50810.472-0.2332-0.1926-0.1759-1.3090.2713-0.1338-0.74310.0920.40280.08440.14890.81910.16420.646117.803126.98760.9665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 19 through 123 )H19 - 123
2X-RAY DIFFRACTION2chain 'H' and (resid 124 through 240 )H124 - 240
3X-RAY DIFFRACTION3chain 'L' and (resid 21 through 133 )L21 - 133
4X-RAY DIFFRACTION4chain 'L' and (resid 134 through 233 )L134 - 233
5X-RAY DIFFRACTION5chain 'A' and (resid 31 through 58 )A31 - 58
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 119 )A59 - 119
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 151 )A120 - 151
8X-RAY DIFFRACTION8chain 'A' and (resid 152 through 176 )A152 - 176
9X-RAY DIFFRACTION9chain 'A' and (resid 177 through 195 )A177 - 195
10X-RAY DIFFRACTION10chain 'A' and (resid 196 through 235 )A196 - 235
11X-RAY DIFFRACTION11chain 'A' and (resid 236 through 316 )A236 - 316
12X-RAY DIFFRACTION12chain 'A' and (resid 317 through 330 )A317 - 330
13X-RAY DIFFRACTION13chain 'A' and (resid 331 through 360 )A331 - 360

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