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- PDB-7jum: Pfs230 D1 domain in complex with neutralizing antibody LMIV230-01 -

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Basic information

Entry
Database: PDB / ID: 7jum
TitlePfs230 D1 domain in complex with neutralizing antibody LMIV230-01
Components
  • Gametocyte surface protein P230
  • Neutralizing antibody, LMIV230-01 Single-chain Fv
KeywordsCELL INVASION / Pfs230D1 / Pfs230 / monoclonal antibody
Function / homology: / 6-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 / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.998 Å
AuthorsTolia, N. / Tang, W.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001236 United States
CitationJournal: Nat Commun / Year: 2021
Title: A human monoclonal antibody blocks malaria transmission and defines a highly conserved neutralizing epitope on gametes.
Authors: Coelho, C.H. / Tang, W.K. / Burkhardt, M. / Galson, J.D. / Muratova, O. / Salinas, N.D. / Alves E Silva, T.L. / Reiter, K. / MacDonald, N.J. / Nguyen, V. / Herrera, R. / Shimp, R. / Narum, D. ...Authors: Coelho, C.H. / Tang, W.K. / Burkhardt, M. / Galson, J.D. / Muratova, O. / Salinas, N.D. / Alves E Silva, T.L. / Reiter, K. / MacDonald, N.J. / Nguyen, V. / Herrera, R. / Shimp, R. / Narum, D.L. / Byrne-Steele, M. / Pan, W. / Hou, X. / Brown, B. / Eisenhower, M. / Han, J. / Jenkins, B.J. / Doritchamou, J.Y.A. / Smelkinson, M.G. / Vega-Rodriguez, J. / Truck, J. / Taylor, J.J. / Sagara, I. / Renn, J.P. / Tolia, N.H. / Duffy, P.E.
History
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gametocyte surface protein P230
B: Gametocyte surface protein P230
C: Gametocyte surface protein P230
H: Neutralizing antibody, LMIV230-01 Single-chain Fv
I: Neutralizing antibody, LMIV230-01 Single-chain Fv
J: Neutralizing antibody, LMIV230-01 Single-chain Fv


Theoretical massNumber of molelcules
Total (without water)147,1086
Polymers147,1086
Non-polymers00
Water19,5641086
1
A: Gametocyte surface protein P230
H: Neutralizing antibody, LMIV230-01 Single-chain Fv


Theoretical massNumber of molelcules
Total (without water)49,0362
Polymers49,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-4 kcal/mol
Surface area18730 Å2
MethodPISA
2
B: Gametocyte surface protein P230
I: Neutralizing antibody, LMIV230-01 Single-chain Fv


Theoretical massNumber of molelcules
Total (without water)49,0362
Polymers49,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-1 kcal/mol
Surface area18350 Å2
MethodPISA
3
C: Gametocyte surface protein P230
J: Neutralizing antibody, LMIV230-01 Single-chain Fv


Theoretical massNumber of molelcules
Total (without water)49,0362
Polymers49,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-3 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.020, 144.020, 54.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains B C
44Chains H I
55Chains H J
66Chains I J

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Gametocyte surface protein P230


Mass: 21881.838 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFS230, PF230, S230 / Production host: Homo sapiens (human) / References: UniProt: P68874
#2: Antibody Neutralizing antibody, LMIV230-01 Single-chain Fv


Mass: 27154.229 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 6.5, 26 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→19.74 Å / Num. obs: 85033 / % possible obs: 99.43 % / Redundancy: 3.22 % / CC1/2: 0.98 / Net I/σ(I): 5.34
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 5629 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.998→19.739 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.199 / SU B: 5.391 / SU ML: 0.143 / Average fsc free: 0.8858 / Average fsc work: 0.8981 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2331 4252 5 %
Rwork0.1909 80781 -
all0.193 --
obs-85033 99.188 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.449 Å2-0.225 Å20 Å2
2---0.449 Å20 Å2
3---1.457 Å2
Refinement stepCycle: LAST / Resolution: 1.998→19.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9429 0 0 1086 10515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139643
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178940
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.65113057
X-RAY DIFFRACTIONr_angle_other_deg1.231.57920904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.73451200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35823.844424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.458151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7821533
X-RAY DIFFRACTIONr_chiral_restr0.0620.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021883
X-RAY DIFFRACTIONr_nbd_refined0.1940.21477
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.27920
X-RAY DIFFRACTIONr_nbtor_refined0.1590.24508
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2847
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.239
X-RAY DIFFRACTIONr_nbd_other0.1780.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.239
X-RAY DIFFRACTIONr_mcbond_it2.4383.2114821
X-RAY DIFFRACTIONr_mcbond_other2.4373.214820
X-RAY DIFFRACTIONr_mcangle_it3.5294.7986011
X-RAY DIFFRACTIONr_mcangle_other3.5294.7986012
X-RAY DIFFRACTIONr_scbond_it3.0513.5394822
X-RAY DIFFRACTIONr_scbond_other3.0513.5394823
X-RAY DIFFRACTIONr_scangle_it4.725.1477045
X-RAY DIFFRACTIONr_scangle_other4.725.1487046
X-RAY DIFFRACTIONr_lrange_it6.60437.24910593
X-RAY DIFFRACTIONr_lrange_other6.52936.80710341
X-RAY DIFFRACTIONr_ncsr_local_group_10.0750.055392
X-RAY DIFFRACTIONr_ncsr_local_group_20.080.055318
X-RAY DIFFRACTIONr_ncsr_local_group_30.0710.055345
X-RAY DIFFRACTIONr_ncsr_local_group_40.0590.056946
X-RAY DIFFRACTIONr_ncsr_local_group_50.0860.056814
X-RAY DIFFRACTIONr_ncsr_local_group_60.0810.056837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.998-2.0490.3842960.33556290.33762600.6810.70994.64860.327
2.049-2.1050.2943070.29458250.29461520.8040.78899.67490.285
2.105-2.1650.3062970.25756380.2659770.8480.85899.29730.246
2.165-2.2310.2752850.24654340.24757750.8530.86499.03030.234
2.231-2.3030.2582770.2152570.21255810.8850.90299.15790.2
2.303-2.3830.2532720.19451610.19754470.9020.91299.7430.187
2.383-2.4720.2522620.18449820.18852510.8990.91899.86670.177
2.472-2.5710.2322530.16948090.17250650.9210.93999.94080.164
2.571-2.6830.2572390.18445460.18847890.9070.92499.91650.181
2.683-2.8110.2292330.17744120.1846510.9160.93499.8710.176
2.811-2.960.2372220.17942170.18244450.9160.93699.8650.18
2.96-3.1350.2342060.18339130.18641360.9210.93799.5890.188
3.135-3.3460.241980.18637640.18839790.9160.94199.57280.193
3.346-3.6050.2251810.18234500.18436390.9420.9599.78020.193
3.605-3.9360.1871690.17432120.17533810.950.9541000.191
3.936-4.3790.2331530.1628930.16430510.9370.95599.83610.187
4.379-5.0160.1871360.1625850.16127270.9610.96699.780.192
5.016-6.0460.191160.1922190.1923450.9570.95699.57360.22
6.046-8.1750.207910.217270.218230.9530.9599.72570.232
8.175-19.7390.209590.18911070.1911690.9550.95399.74340.223

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