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- PDB-7zxg: Pfs48/45 bound to Fab fragment of monoclonal antibody 10D8 -

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Basic information

Entry
Database: PDB / ID: 7zxg
TitlePfs48/45 bound to Fab fragment of monoclonal antibody 10D8
Components
  • 10D8 heavy chain
  • 10D8 light chain
  • Gametocyte surface protein P45/48
KeywordsCELL ADHESION / Pfs48/45 / malaria / transmission-blocking / Plasmodium falciparum / gamete / antibody
Function / homology6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / side of membrane / cell surface / plasma membrane / Gametocyte surface protein P45/48
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsKo, K.T. / Lennartz, F.L. / Higgins, M.K.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R001138/1 United Kingdom
Wellcome Trust218482/Z/19/Z United Kingdom
Wellcome Trust101020/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the malaria vaccine candidate Pfs48/45 and its recognition by transmission blocking antibodies.
Authors: Ko, K.T. / Lennartz, F. / Mekhaiel, D. / Guloglu, B. / Marini, A. / Deuker, D.J. / Long, C.A. / Jore, M.M. / Miura, K. / Biswas, S. / Higgins, M.K.
History
DepositionMay 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P45/48
B: 10D8 heavy chain
C: 10D8 light chain
D: Gametocyte surface protein P45/48
E: 10D8 heavy chain
F: 10D8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,45813
Polymers254,4076
Non-polymers3,0517
Water00
1
A: Gametocyte surface protein P45/48
B: 10D8 heavy chain
C: 10D8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8197
Polymers127,2043
Non-polymers1,6154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Gametocyte surface protein P45/48
E: 10D8 heavy chain
F: 10D8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6396
Polymers127,2043
Non-polymers1,4353
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.771, 125.803, 216.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and (resid 2 through 124 or resid 126...
d_2ens_1(chain "E" and (resid 2 through 124 or resid 126...
d_1ens_2(chain "C" and (resid 1 through 23 or resid 25...
d_2ens_2(chain "F" and (resid 1 through 23 or resid 25...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALALAB1 - 123
d_12ens_1THRGLYB125 - 136
d_13ens_1SERPROB138 - 151
d_14ens_1PROTHRB153 - 191
d_15ens_1PROTHRB193 - 196
d_16ens_1THRSERB198 - 206
d_17ens_1VALLYSB210 - 212
d_21ens_1VALALAE1 - 123
d_22ens_1THRGLYE125 - 136
d_23ens_1SERPROE140 - 153
d_24ens_1PROTHRE155 - 193
d_25ens_1PROTHRE195 - 198
d_26ens_1THRSERE200 - 208
d_27ens_1VALLYSE212 - 214
d_11ens_2ASPCYSC1 - 23
d_12ens_2SERLYSC25 - 85
d_13ens_2ASPILEC88 - 112
d_14ens_2ARGLEUC114 - 131
d_15ens_2SERTRPC133 - 154
d_16ens_2GLYASNC164 - 216
d_21ens_2ASPCYSF1 - 23
d_22ens_2SERLYSF25 - 85
d_23ens_2ASPILEF88 - 112
d_24ens_2ARGLEUF114 - 131
d_25ens_2SERTRPF133 - 154
d_26ens_2GLYASNF156 - 208

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.533054048146, 0.348372814131, -0.771031623301), (-0.388976393926, 0.910186941943, 0.142327424217), (0.751365920656, 0.224044890793, 0.620687634955)20.9246116747, -61.2762565283, 6.22295079184
2given(0.535035923136, 0.336745213471, -0.774815605262), (-0.37072738495, 0.917691423066, 0.142841373832), (0.759142784331, 0.210820096848, 0.615838550079)20.9405778009, -61.5057290152, 5.85788430636

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Gametocyte surface protein P45/48 / Pfs48/45


Mass: 49180.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF45/48, PFS45-48, PFS45/48, PF13_0247, PF3D7_1346700 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8I6T1

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Antibody , 2 types, 4 molecules BECF

#2: Antibody 10D8 heavy chain


Mass: 51485.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody 10D8 light chain


Mass: 26537.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 4 types, 7 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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


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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Details

Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10 % (w/v) PEG 1000 and 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 4.2→76.27 Å / Num. obs: 109594 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 171.07 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.088 / Net I/σ(I): 7.5
Reflection shellResolution: 4.2→4.7 Å / Num. unique obs: 31747 / CC1/2: 0.543 / Rpim(I) all: 0.668

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H5N

6h5n


Resolution: 4.2→65.36 Å / SU ML: 0.6066 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.2274
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2761 1691 10 %
Rwork0.2593 15226 -
obs0.261 16917 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 212.14 Å2
Refinement stepCycle: LAST / Resolution: 4.2→65.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12398 0 201 0 12599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002912891
X-RAY DIFFRACTIONf_angle_d0.642217487
X-RAY DIFFRACTIONf_chiral_restr0.05072001
X-RAY DIFFRACTIONf_plane_restr0.00392194
X-RAY DIFFRACTIONf_dihedral_angle_d14.34194720
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JX-RAY DIFFRACTIONTorsion NCS1.14531795754
ens_2d_2KX-RAY DIFFRACTIONTorsion NCS1.08967608095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.320.37481390.35241247X-RAY DIFFRACTION99.71
4.32-4.460.3361360.33231228X-RAY DIFFRACTION99.56
4.46-4.620.31651390.30491249X-RAY DIFFRACTION99.86
4.62-4.810.28961400.2931260X-RAY DIFFRACTION99.72
4.81-5.030.28851380.27111242X-RAY DIFFRACTION100
5.03-5.290.25951380.26021243X-RAY DIFFRACTION100
5.29-5.620.3181390.2831253X-RAY DIFFRACTION99.93
5.62-6.060.31581420.28741275X-RAY DIFFRACTION99.93
6.06-6.670.30751410.2791270X-RAY DIFFRACTION99.93
6.67-7.630.30481430.28921284X-RAY DIFFRACTION99.72
7.63-9.60.23951440.23621298X-RAY DIFFRACTION99.93
9.61-65.360.23531520.21051377X-RAY DIFFRACTION99.03
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)
12.27462774155-1.503454990270.3820098386454.730181332080.6682117506663.61370348216-0.0568084677104-0.6416244905270.1659279218960.1898469440110.1925888581920.387003506441-0.4337437609340.0954518075691-0.1590778100361.527879840310.1292390630070.01793555058791.81987673108-0.4498020616231.88700110892-6.27502258296-7.479901911874.2249394867
21.87239203612-1.911189018560.0210737003962.898376989481.808573036553.32785934785-0.428143585353-0.2151545121540.6365632710480.3716296335730.353300458803-0.0577820536732-0.66720157621-0.116532232008-0.04810344867161.601820166960.0177313661724-0.08037026498491.02000773092-0.05149155214491.3679583700511.700776896-34.00780170428.7444851377
31.14909820573-1.0137557829-2.54116719292.536203616423.896592982647.079557290210.09907263749450.0808443846897-0.00264699592083-0.757598810133-0.2010830231250.0344699491891-1.45742972219-0.5746455739510.25157104951.770835098440.132816452284-0.1679320079611.714965739050.005446941357491.673276646194.88796245381-28.900812865312.648168922
42.198488030540.694476648691-0.5302940793732.95380926244-2.391474009971.81603030382-0.208040514587-0.0336602898680.5809723519660.2907922107990.1958972711430.65148784806-0.406414514524-0.585272528653-0.07695342873741.989741552030.3484838625110.07038045821091.7109121023-0.2714788095821.95751541728-39.4551835898-55.990606859446.7076974855
54.72471799943-1.34610177317-2.709224312533.87410465662-0.2094549399476.90812822809-0.953878927141-0.362094995648-1.27486466964-0.05697198035620.137699559164-0.1617823819340.8684998918611.059511695980.7991438415481.54755187422-0.1246048642980.2284979698111.58994778090.09373270066781.76878275203-7.12379902666-92.149344722125.2110385333
64.92214557022-1.52828860198-1.545515198873.022449552710.3776565446962.396343610760.03647854654830.0887107503871-0.862769889613-1.21399916909-0.14813501267-1.542679434080.3933666151680.5179273555670.1139624927281.83677595520.0620300105860.6379552221362.007560838410.02275817856552.423462015913.87995289048-86.986395826811.7285782169
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 45 through 428)AA45 - 4281 - 363
22(chain 'B' and resid 2 through 224)BB2 - 2241 - 218
33(chain 'C' and resid 1 through 217)CC1 - 2171 - 217
44(chain 'D' and resid 45 through 428)DD45 - 4281 - 352
55(chain 'E' and resid 2 through 219)EE2 - 2191 - 215
66(chain 'F' and resid 1 through 217)FF1 - 2171 - 209

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