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- PDB-9c7f: Human monoclonal antibody MAD24-01 bound to the N-terminus of cle... -

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Basic information

Entry
Database: PDB / ID: 9c7f
TitleHuman monoclonal antibody MAD24-01 bound to the N-terminus of cleaved circumsporozoite protein
Components
  • Circumsporozoite protein
  • Monoclonal antibody MAD24-01 Fab Heavy Chain
  • Monoclonal antibody MAD24-01 Fab Light Chain
KeywordsIMMUNE SYSTEM / Antibody / malaria
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
: / Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMoskovitz, R. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationDAC-1601-INV-056202 United States
CitationJournal: Science / Year: 2025
Title: Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein.
Authors: Dacon, C. / Moskovitz, R. / Swearingen, K. / Da Silva Pereira, L. / Flores-Garcia, Y. / Aleshnick, M. / Kanatani, S. / Flynn, B. / Molina-Cruz, A. / Wollenberg, K. / Traver, M. / Kirtley, P. ...Authors: Dacon, C. / Moskovitz, R. / Swearingen, K. / Da Silva Pereira, L. / Flores-Garcia, Y. / Aleshnick, M. / Kanatani, S. / Flynn, B. / Molina-Cruz, A. / Wollenberg, K. / Traver, M. / Kirtley, P. / Purser, L. / Dillon, M. / Bonilla, B. / Franco, A. / Petros, S. / Kritzberg, J. / Tucker, C. / Paez, G.G. / Gupta, P. / Shears, M.J. / Pazzi, J. / Edgar, J.M. / Teng, A.A. / Belmonte, A. / Oda, K. / Doumbo, S. / Krymskaya, L. / Skinner, J. / Li, S. / Ghosal, S. / Kayentao, K. / Ongoiba, A. / Vaughan, A. / Campo, J.J. / Traore, B. / Barillas-Mury, C. / Wijayalath, W. / Idris, A. / Crompton, P.D. / Sinnis, P. / Wilder, B.K. / Zavala, F. / Seder, R.A. / Wilson, I.A. / Tan, J.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Monoclonal antibody MAD24-01 Fab Heavy Chain
L: Monoclonal antibody MAD24-01 Fab Light Chain
A: Monoclonal antibody MAD24-01 Fab Heavy Chain
B: Monoclonal antibody MAD24-01 Fab Light Chain
C: Monoclonal antibody MAD24-01 Fab Heavy Chain
D: Monoclonal antibody MAD24-01 Fab Light Chain
E: Monoclonal antibody MAD24-01 Fab Heavy Chain
F: Monoclonal antibody MAD24-01 Fab Light Chain
Q: Circumsporozoite protein
G: Circumsporozoite protein
I: Circumsporozoite protein
J: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,68916
Polymers196,40612
Non-polymers2,2824
Water25,4731414
1
H: Monoclonal antibody MAD24-01 Fab Heavy Chain
L: Monoclonal antibody MAD24-01 Fab Light Chain
J: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6724
Polymers49,1023
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Monoclonal antibody MAD24-01 Fab Heavy Chain
B: Monoclonal antibody MAD24-01 Fab Light Chain
G: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6724
Polymers49,1023
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Monoclonal antibody MAD24-01 Fab Heavy Chain
D: Monoclonal antibody MAD24-01 Fab Light Chain
I: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6724
Polymers49,1023
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Monoclonal antibody MAD24-01 Fab Heavy Chain
F: Monoclonal antibody MAD24-01 Fab Light Chain
Q: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6724
Polymers49,1023
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.541, 88.320, 168.952
Angle α, β, γ (deg.)90.000, 89.745, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 6 or resid 8...
d_2ens_1(chain "C" and (resid 1 through 6 or resid 8...
d_3ens_1(chain "E" and (resid 1 through 6 or resid 8...
d_4ens_1(chain "H" and (resid 1 through 6 or resid 8...
d_1ens_2(chain "B" and (resid 1 through 11 or resid 13...
d_2ens_2(chain "D" and (resid 1 through 11 or resid 13...
d_3ens_2(chain "F" and (resid 1 through 11 or resid 13...
d_4ens_2(chain "L" and (resid 1 through 11 or resid 13...
d_1ens_3chain "G"
d_2ens_3chain "I"
d_3ens_3chain "J"
d_4ens_3chain "Q"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PCAPCAGLUGLUAC1 - 61 - 6
d_12ens_1GLYGLYLEULEUAC8 - 208 - 20
d_13ens_1CYSCYSVALVALAC22 - 4822 - 48
d_14ens_1TYRTYRLEULEUAC50 - 17850 - 187
d_15ens_1SERSERPROPROAC180 - 185189 - 194
d_16ens_1SERSERLYSLYSAC187 - 214196 - 223
d_21ens_1PCAPCAGLUGLUCE1 - 61 - 6
d_22ens_1GLYGLYLEULEUCE8 - 208 - 20
d_23ens_1CYSCYSVALVALCE22 - 4822 - 48
d_24ens_1TYRTYRLEULEUCE50 - 17850 - 187
d_25ens_1SERSERPROPROCE180 - 185189 - 194
d_26ens_1SERSERLYSLYSCE187 - 214196 - 223
d_31ens_1PCAPCAGLUGLUEG1 - 61 - 6
d_32ens_1GLYGLYLEULEUEG8 - 208 - 20
d_33ens_1CYSCYSVALVALEG22 - 4822 - 48
d_34ens_1TYRTYRLEULEUEG50 - 17850 - 187
d_35ens_1SERSERPROPROEG180 - 185189 - 194
d_36ens_1SERSERLYSLYSEG187 - 214196 - 223
d_41ens_1PCAPCAGLUGLUHA1 - 61 - 6
d_42ens_1GLYGLYLEULEUHA8 - 208 - 20
d_43ens_1CYSCYSVALVALHA22 - 4822 - 48
d_44ens_1TYRTYRLEULEUHA50 - 17850 - 187
d_45ens_1SERSERPROPROHA180 - 185189 - 194
d_46ens_1SERSERLYSLYSHA187 - 214196 - 223
d_11ens_2GLUGLULEULEUBD1 - 111 - 11
d_12ens_2LEULEUGLUGLUBD13 - 1713 - 17
d_13ens_2ALAALAPROPROBD19 - 4419 - 44
d_14ens_2LEULEULEULEUBD46 - 4746 - 47
d_15ens_2TYRTYRPHEPHEBD49 - 7149 - 71
d_16ens_2LEULEUPROPROBD73 - 11373 - 113
d_17ens_2VALVALGLUGLUBD115 - 211115 - 211
d_18ens_2NAGNAGNAGNAGMN1
d_21ens_2GLUGLULEULEUDF1 - 111 - 11
d_22ens_2LEULEUGLUGLUDF13 - 1713 - 17
d_23ens_2ALAALAPROPRODF19 - 4419 - 44
d_24ens_2LEULEULEULEUDF46 - 4746 - 47
d_25ens_2TYRTYRPHEPHEDF49 - 7149 - 71
d_26ens_2LEULEUPROPRODF73 - 11373 - 113
d_27ens_2VALVALGLUGLUDF115 - 211115 - 211
d_28ens_2NAGNAGNAGNAGNO1
d_31ens_2GLUGLULEULEUFH1 - 111 - 11
d_32ens_2LEULEUGLUGLUFH13 - 1713 - 17
d_33ens_2ALAALAPROPROFH19 - 4419 - 44
d_34ens_2LEULEULEULEUFH46 - 4746 - 47
d_35ens_2TYRTYRPHEPHEFH49 - 7149 - 71
d_36ens_2LEULEUPROPROFH73 - 11373 - 113
d_37ens_2VALVALGLUGLUFH115 - 211115 - 211
d_38ens_2NAGNAGNAGNAGOP1
d_41ens_2GLUGLULEULEULB1 - 111 - 11
d_42ens_2LEULEUGLUGLULB13 - 1713 - 17
d_43ens_2ALAALAPROPROLB19 - 4419 - 44
d_44ens_2LEULEULEULEULB46 - 4746 - 47
d_45ens_2TYRTYRPHEPHELB49 - 7149 - 71
d_46ens_2LEULEUPROPROLB73 - 11373 - 113
d_47ens_2VALVALGLUGLULB115 - 211115 - 211
d_48ens_2NAGNAGNAGNAGKM1
d_11ens_3PCAPCAASPASPGJ12 - 191 - 8
d_21ens_3PCAPCAASPASPIK196 - 2031 - 8
d_31ens_3PCAPCAASPASPJL310 - 3171 - 8
d_41ens_3PCAPCAASPASPQI3 - 101 - 8

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.999265773625, -0.0278053299047, 0.0263586283965), (0.0293814234081, -0.997679222636, 0.0614239422214), (0.0245895429109, 0.0621532971643, 0.997763660408)110.910905259, -78.33865672, 42.95783417
2given(0.999466029567, 0.0212375480132, -0.0248318806349), (0.0230685850019, -0.996845569213, 0.0759391304034), (-0.0231407892581, -0.0764714175022, -0.996803203334)-36.1559220091, -120.530744453, 40.9693309013
3given(-0.99972285139, -0.0158494473071, 0.0174073383532), (-0.0163540776726, 0.999438617492, -0.0292402806044), (-0.0169341238913, -0.0295168576648, -0.99942082756)74.1712059397, 43.7784650513, 84.4482088706
4given(-0.999495815893, -0.0309048561288, 0.00728037640807), (0.0312629639979, -0.997958618132, 0.0556886306061), (0.00554446526279, 0.0558881594291, 0.998421640661)111.4335529, -78.0266740514, 43.5861281906
5given(0.999764756504, 0.0216887048485, -0.000178140917774), (0.021637676327, -0.99677817723, 0.0772339068095), (0.00149753642978, -0.0772195925908, -0.997012984823)-36.9415100571, -120.181655063, 39.8431604391
6given(-0.999815583456, -0.0188638903146, 0.00359898889229), (-0.0189476349251, 0.999511387762, -0.0248590599979), (-0.00312829180115, -0.0249226679036, -0.999684487433)74.470743236, 43.5518496886, 83.9120062717
7given(-0.999905841756, -0.0115276531697, 0.00744451702745), (0.0118978549976, -0.998588504703, 0.0517633009128), (0.00683729974684, 0.0518470007554, 0.998631633709)112.954266618, -77.0795084031, 43.0590166414
8given(-0.999771554191, 0.0185468720038, 0.010623227788), (0.0184082526065, 0.999746020927, -0.0130011490703), (-0.0108616603582, -0.0128026239517, -0.999859048643)76.6767143065, 41.2422620985, 85.2622098817
9given(0.99578344245, -0.0533884573523, -0.0745989836596), (-0.0415312803463, -0.987458621842, 0.152317506879), (-0.0817954063154, -0.148577060042, -0.985512236725)-39.7425767532, -117.855595976, 40.159951977

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Components

#1: Antibody
Monoclonal antibody MAD24-01 Fab Heavy Chain


Mass: 23996.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
Monoclonal antibody MAD24-01 Fab Light Chain


Mass: 23275.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide
Circumsporozoite protein / CS / PfCSP


Mass: 1828.804 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q7K740
#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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1414 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350 and 0.2 M potassium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.82→45 Å / Num. obs: 192978 / % possible obs: 97.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.079 / Net I/σ(I): 3.6
Reflection shellResolution: 1.82→1.84 Å / Rmerge(I) obs: 1.024 / Num. unique obs: 9564 / CC1/2: 0.306 / Rpim(I) all: 0.482

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→45 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4468
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 9529 4.97 %
Rwork0.2106 182235 -
obs0.2119 191764 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.58 Å2
Refinement stepCycle: LAST / Resolution: 1.82→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13448 0 152 1414 15014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003914062
X-RAY DIFFRACTIONf_angle_d0.820519150
X-RAY DIFFRACTIONf_chiral_restr0.04742168
X-RAY DIFFRACTIONf_plane_restr0.00512452
X-RAY DIFFRACTIONf_dihedral_angle_d13.50245018
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS1.10153805877
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.986316787454
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS0.450271217525
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS0.910498205115
ens_2d_3DBX-RAY DIFFRACTIONTorsion NCS0.855497042173
ens_2d_4DBX-RAY DIFFRACTIONTorsion NCS0.60683323078
ens_3d_2JGX-RAY DIFFRACTIONTorsion NCS0.480134076886
ens_3d_3JGX-RAY DIFFRACTIONTorsion NCS0.567760215785
ens_3d_4JGX-RAY DIFFRACTIONTorsion NCS1.25819756723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.38681390.36812930X-RAY DIFFRACTION46.87
1.84-1.860.35993180.35316054X-RAY DIFFRACTION97.58
1.86-1.880.33883270.33866051X-RAY DIFFRACTION98.68
1.88-1.910.33533420.3186116X-RAY DIFFRACTION98.61
1.91-1.930.34083150.30296108X-RAY DIFFRACTION98.97
1.93-1.960.29412960.29586213X-RAY DIFFRACTION98.98
1.96-1.990.31973220.28416108X-RAY DIFFRACTION99.17
1.99-2.020.29962950.27766200X-RAY DIFFRACTION99.13
2.02-2.050.2813630.26736075X-RAY DIFFRACTION99.34
2.05-2.080.28043270.26116161X-RAY DIFFRACTION99.07
2.08-2.120.26023290.25086125X-RAY DIFFRACTION99.17
2.12-2.160.29182690.23396237X-RAY DIFFRACTION99.48
2.16-2.20.2683350.23466168X-RAY DIFFRACTION99.31
2.2-2.240.26593390.22586133X-RAY DIFFRACTION99.43
2.24-2.290.27933370.22136139X-RAY DIFFRACTION99.46
2.29-2.350.27193270.21956205X-RAY DIFFRACTION99.35
2.35-2.40.25323270.21076196X-RAY DIFFRACTION99.45
2.4-2.470.24093090.20616159X-RAY DIFFRACTION99.54
2.47-2.540.24123130.20226194X-RAY DIFFRACTION99.57
2.54-2.620.23633550.19716203X-RAY DIFFRACTION99.61
2.62-2.720.2293350.20186164X-RAY DIFFRACTION99.79
2.72-2.830.2372840.19916242X-RAY DIFFRACTION99.62
2.83-2.950.23553040.19466248X-RAY DIFFRACTION99.71
2.95-3.110.20573380.19876222X-RAY DIFFRACTION99.65
3.11-3.30.22253380.20286223X-RAY DIFFRACTION99.92
3.3-3.560.22213450.18736206X-RAY DIFFRACTION99.85
3.56-3.920.1853410.18276236X-RAY DIFFRACTION99.91
3.92-4.480.1773330.15396252X-RAY DIFFRACTION99.88
4.48-5.650.18183200.14866307X-RAY DIFFRACTION99.85
5.65-450.2323070.20466360X-RAY DIFFRACTION98.55

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