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- PDB-2z8w: Structure of an IgNAR-AMA1 complex -

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Basic information

Entry
Database: PDB / ID: 2z8w
TitleStructure of an IgNAR-AMA1 complex
Components
  • Apical membrane antigen 1
  • New antigen receptor variable domain
KeywordsIMMUNE SYSTEM / AMA1-VNAR complex / 14I1-M15 / Receptor
Function / homology
Function and homology information


apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Immunoglobulin V-Type / Immunoglobulin V-set domain / 3-Layer(bba) Sandwich / Immunoglobulin V-set domain ...Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Immunoglobulin V-Type / Immunoglobulin V-set domain / 3-Layer(bba) Sandwich / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
New antigen receptor variable domain / Apical membrane antigen 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Orectolobus maculatus (spotted wobbegong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsStreltsov, V.A. / Henderson, K.A. / Batchelor, A.H. / Coley, A.M. / Nuttall, S.D.
CitationJournal: Structure / Year: 2007
Title: Structure of an IgNAR-AMA1 Complex: Targeting a Conserved Hydrophobic Cleft Broadens Malarial Strain Recognition
Authors: Henderson, K.A. / Streltsov, V.A. / Coley, A.M. / Dolezal, O. / Hudson, P.J. / Batchelor, A.H. / Gupta, A. / Bai, T. / Murphy, V.J. / Anders, R.F. / Foley, M. / Nuttall, S.D.
History
DepositionSep 11, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apical membrane antigen 1
B: Apical membrane antigen 1
C: New antigen receptor variable domain
D: New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)102,4434
Polymers102,4434
Non-polymers00
Water8,575476
1
A: Apical membrane antigen 1
D: New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)51,2212
Polymers51,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
MethodPISA
2
B: Apical membrane antigen 1
C: New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)51,2212
Polymers51,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.480, 76.480, 140.978
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Apical membrane antigen 1 /


Mass: 38360.047 Da / Num. of mol.: 2 / Fragment: domain I, II, UNP residues 104-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: pPROEXHTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7KQK5
#2: Protein New antigen receptor variable domain


Mass: 12861.390 Da / Num. of mol.: 2 / Mutation: P90L/G92R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong)
Plasmid: pGC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6X1E6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M phosphate citrate pH 4.2, 0.2M NaCl, 20% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.96426 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2006 / Details: mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96426 Å / Relative weight: 1
ReflectionResolution: 2.45→66.23 Å / Num. all: 28622 / Num. obs: 28622 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.4
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1Z40 and 1VER

1z40

1ver


Resolution: 2.45→38.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.865 / SU B: 23.776 / SU ML: 0.289 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28183 3222 10.1 %RANDOM
Rwork0.18877 ---
obs0.19822 28622 93.94 %-
all-28622 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.778 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å21.08 Å20 Å2
2--2.15 Å20 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7198 0 0 476 7674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.341.959984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04524.807362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.484151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3311534
X-RAY DIFFRACTIONr_chiral_restr0.0990.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025674
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23550
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24901
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2489
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5381.54601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93427234
X-RAY DIFFRACTIONr_scbond_it1.21733189
X-RAY DIFFRACTIONr_scangle_it1.884.52750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 165 -
Rwork0.247 1464 -
obs--64.85 %
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)
13.9409-0.2910.36841.78230.0891.62320.1220.2801-0.4579-0.0931-0.0644-0.12840.11380.203-0.0577-0.426-0.0292-0.0359-0.4163-0.10960.115727.432-11.417-14.69
22.0365-0.71460.23413.3385-0.23561.4150.05490.1026-0.3106-0.30720.03390.35620.208-0.004-0.0888-0.41830.0269-0.123-0.4697-0.01790.09873.851-29.519-38.189
37.383-0.8323-0.93713.96890.20833.0730.1124-0.0786-0.0684-0.2623-0.09630.3807-0.01480.0699-0.0161-0.29020.0729-0.0158-0.4870.05120.009727.661-53.992-34.288
45.68442.1213-0.02414.8077-0.4392.28130.08610.26-0.38290.0243-0.07090.01670.00850.0189-0.0151-0.40820.0375-0.0225-0.26410.01130.04160.701-2.978-10.785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA104 - 4381 - 335
2X-RAY DIFFRACTION2BB104 - 4381 - 335
3X-RAY DIFFRACTION3CC1 - 1161 - 116
4X-RAY DIFFRACTION4DD1 - 1161 - 116

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