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- PDB-6o25: Crystal structure of 3945 Fab in complex with circumsporozoite pr... -

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Basic information

Entry
Database: PDB / ID: 6o25
TitleCrystal structure of 3945 Fab in complex with circumsporozoite protein NANP3 and anti-Kappa VHH domain
Components
  • 3945 Fab heavy chain
  • 3945 Kappa light chain
  • Anti-Kappa VHH domain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / 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)
Lama glama (llama)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsScally, S.W. / Bosch, A. / Prieto, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Nat. Med. / Year: 2020
Title: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs.
Authors: Murugan, R. / Scally, S.W. / Costa, G. / Mustafa, G. / Thai, E. / Decker, T. / Bosch, A. / Prieto, K. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3945 Fab heavy chain
E: 3945 Fab heavy chain
F: 3945 Kappa light chain
B: 3945 Kappa light chain
I: 3945 Fab heavy chain
J: 3945 Kappa light chain
K: Anti-Kappa VHH domain
C: Anti-Kappa VHH domain
G: Anti-Kappa VHH domain
D: Circumsporozoite protein
H: Circumsporozoite protein
L: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)180,05512
Polymers180,05512
Non-polymers00
Water543
1
A: 3945 Fab heavy chain
B: 3945 Kappa light chain
C: Anti-Kappa VHH domain
D: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)60,0184
Polymers60,0184
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 3945 Fab heavy chain
F: 3945 Kappa light chain
G: Anti-Kappa VHH domain
H: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)60,0184
Polymers60,0184
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: 3945 Fab heavy chain
J: 3945 Kappa light chain
K: Anti-Kappa VHH domain
L: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)60,0184
Polymers60,0184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.249, 230.737, 48.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain E and (resid 1 through 74 or (resid 75...
31(chain I and ((resid 1 and (name N or name...
12(chain B and (resid 1 through 76 or (resid 77...
22(chain F and (resid 1 through 76 or (resid 77...
32(chain J and (resid 1 through 125 or (resid 126...
13chain C
23chain G
33chain K
14(chain D and resid 2 through 11)
24chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLNGLN(chain A and ((resid 1 and (name N or name...AA11
121GLNGLNPROPRO(chain A and ((resid 1 and (name N or name...AA1 - 2131 - 221
131GLNGLNPROPRO(chain A and ((resid 1 and (name N or name...AA1 - 2131 - 221
141GLNGLNPROPRO(chain A and ((resid 1 and (name N or name...AA1 - 2131 - 221
151GLNGLNPROPRO(chain A and ((resid 1 and (name N or name...AA1 - 2131 - 221
211GLNGLNSERSER(chain E and (resid 1 through 74 or (resid 75...EB1 - 741 - 75
221LYSLYSLYSLYS(chain E and (resid 1 through 74 or (resid 75...EB7576
231GLNGLNPROPRO(chain E and (resid 1 through 74 or (resid 75...EB1 - 2131 - 221
241GLNGLNPROPRO(chain E and (resid 1 through 74 or (resid 75...EB1 - 2131 - 221
251GLNGLNPROPRO(chain E and (resid 1 through 74 or (resid 75...EB1 - 2131 - 221
311GLNGLNGLNGLN(chain I and ((resid 1 and (name N or name...IE11
321GLNGLNPROPRO(chain I and ((resid 1 and (name N or name...IE1 - 2131 - 221
331GLNGLNPROPRO(chain I and ((resid 1 and (name N or name...IE1 - 2131 - 221
341GLNGLNPROPRO(chain I and ((resid 1 and (name N or name...IE1 - 2131 - 221
351GLNGLNPROPRO(chain I and ((resid 1 and (name N or name...IE1 - 2131 - 221
112GLUGLUSERSER(chain B and (resid 1 through 76 or (resid 77...BD1 - 761 - 77
122ARGARGARGARG(chain B and (resid 1 through 76 or (resid 77...BD7778
132GLUGLUGLYGLY(chain B and (resid 1 through 76 or (resid 77...BD1 - 2121 - 213
142GLUGLUGLYGLY(chain B and (resid 1 through 76 or (resid 77...BD1 - 2121 - 213
152GLUGLUGLYGLY(chain B and (resid 1 through 76 or (resid 77...BD1 - 2121 - 213
212GLUGLUSERSER(chain F and (resid 1 through 76 or (resid 77...FC1 - 761 - 77
222ARGARGARGARG(chain F and (resid 1 through 76 or (resid 77...FC7778
232GLUGLUGLUGLU(chain F and (resid 1 through 76 or (resid 77...FC1 - 2131 - 214
242GLUGLUGLUGLU(chain F and (resid 1 through 76 or (resid 77...FC1 - 2131 - 214
252GLUGLUGLUGLU(chain F and (resid 1 through 76 or (resid 77...FC1 - 2131 - 214
262GLUGLUGLUGLU(chain F and (resid 1 through 76 or (resid 77...FC1 - 2131 - 214
312GLUGLULEULEU(chain J and (resid 1 through 125 or (resid 126...JF1 - 1251 - 126
322LYSLYSLYSLYS(chain J and (resid 1 through 125 or (resid 126...JF126127
332GLUGLUGLUGLU(chain J and (resid 1 through 125 or (resid 126...JF1 - 2131 - 214
342GLUGLUGLUGLU(chain J and (resid 1 through 125 or (resid 126...JF1 - 2131 - 214
352GLUGLUGLUGLU(chain J and (resid 1 through 125 or (resid 126...JF1 - 2131 - 214
362GLUGLUGLUGLU(chain J and (resid 1 through 125 or (resid 126...JF1 - 2131 - 214
113VALVALSERSERchain CCH2 - 1122 - 120
213VALVALSERSERchain GGI2 - 1122 - 120
313VALVALSERSERchain KKG2 - 1122 - 120
114ALAALAASNASN(chain D and resid 2 through 11)DJ2 - 112 - 11
214ALAALAASNASNchain LLL2 - 112 - 11

NCS ensembles :
ID
1
2
3
4

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Components

#1: Antibody 3945 Fab heavy chain


Mass: 24126.916 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 3945 Kappa light chain


Mass: 23357.857 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: Antibody Anti-Kappa VHH domain


Mass: 11326.253 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide Circumsporozoite protein / / CS


Mass: 1207.210 Da / Num. of mol.: 3 / Fragment: residues 148-159 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-sodium hydrogen phosphate, 20 % (w/v) PEG 3350

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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: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 39925 / % possible obs: 99.9 % / Redundancy: 14.8 % / Biso Wilson estimate: 50.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.065 / Net I/σ(I): 10
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1998 / CC1/2: 0.664 / Rpim(I) all: 0.221 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Inhouse model

Resolution: 2.9→39.733 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 1989 4.99 %
Rwork0.2153 37838 -
obs0.218 39827 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.41 Å2 / Biso mean: 48.8345 Å2 / Biso min: 8.8 Å2
Refinement stepCycle: final / Resolution: 2.9→39.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12133 0 0 3 12136
Biso mean---20.97 -
Num. residues----1681
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2917X-RAY DIFFRACTION8.518TORSIONAL
12E2917X-RAY DIFFRACTION8.518TORSIONAL
13I2917X-RAY DIFFRACTION8.518TORSIONAL
21B3008X-RAY DIFFRACTION8.518TORSIONAL
22F3008X-RAY DIFFRACTION8.518TORSIONAL
23J3008X-RAY DIFFRACTION8.518TORSIONAL
31C1685X-RAY DIFFRACTION8.518TORSIONAL
32G1685X-RAY DIFFRACTION8.518TORSIONAL
33K1685X-RAY DIFFRACTION8.518TORSIONAL
41D78X-RAY DIFFRACTION8.518TORSIONAL
42L78X-RAY DIFFRACTION8.518TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.97250.38481390.35962652100
2.9725-3.05280.32481410.31032666100
3.0528-3.14260.35051390.28042650100
3.1426-3.2440.30431410.27012676100
3.244-3.35990.33861390.26342634100
3.3599-3.49440.30861410.25482697100
3.4944-3.65330.32841400.25662647100
3.6533-3.84580.29151420.2242679100
3.8458-4.08650.25831420.2042714100
4.0865-4.40160.24771430.16572708100
4.4016-4.84390.22861410.14832712100
4.8439-5.54320.21631440.15932709100
5.5432-6.97770.23451460.19492791100
6.9777-39.7330.21821510.2134290399
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)
15.38240.8801-1.17373.0474-1.18583.08310.00010.016-0.25120.08260.0560.10660.0933-0.0793-0.06630.3768-0.05990.03790.1694-0.00580.2439-26.9663.30324.1889
22.62952.6855-1.41166.5088-0.82673.22820.03490.0696-0.01730.30380.0228-0.1024-0.28530.169-0.02980.363-0.03910.01940.2848-0.05970.22422.993822.701916.4595
34.541-0.15691.44622.98141.0571.5865-0.06110.136-0.2438-0.3047-0.0499-0.94190.0656-0.01030.16580.5615-0.01340.2560.22570.02380.6805-46.465-32.7593-22.0427
43.0641-1.6751-0.76365.46121.20391.5880.0302-0.1720.2108-0.5539-0.12120.1353-0.3924-0.51130.07850.60440.0583-0.07170.3588-0.01570.2548-78.5867-18.3751-14.2524
54.7167-0.458-2.01115.49691.16113.67670.1401-0.3148-0.25040.0505-0.2614-0.8825-0.06930.35180.01550.3237-0.0591-0.06340.32180.12340.4753-42.2845-17.2047-6.0935
63.3762.57191.64272.15170.62133.0250.1209-0.7295-0.10240.1248-0.28130.01370.2326-0.73040.1410.46770.0080.00230.676-0.07720.2907-76.8016-19.31572.2104
73.44061.264-0.54014.8131-1.96862.4298-0.05630.30060.2883-0.33010.32670.53270.2693-0.4804-0.21410.3212-0.09750.00560.39780.02720.2356-33.41917.76828.0308
85.4171-1.65251.53752.4327-0.35662.64830.02290.2481-0.3467-0.0696-0.1489-0.01810.27210.51380.12520.4067-0.03390.0540.36860.02910.18540.952420.84180.3187
95.3114-1.2877-1.06092.34391.79582.7091-0.18470.0429-0.3613-0.27480.2572-0.47280.18850.1327-0.0080.49610.13190.19310.27850.02830.395-51.610938.544-24.3094
102.8991-1.0445-1.47594.2285-0.07240.83740.0734-0.17440.1009-0.6822-0.01020.2175-0.1819-0.0619-0.03790.50130.0837-0.11130.2989-0.0370.2358-81.451257.5706-16.882
113.7151-0.5309-1.52315.52521.99881.8365-0.2755-0.7557-0.03230.4480.4803-0.92070.20830.6477-0.13910.38070.1556-0.01670.5277-0.02670.4106-45.5352.669-7.6086
124.93122.8651.33933.55370.37370.83670.0804-0.3023-0.2338-0.0106-0.16130.01880.299-0.16430.08070.37930.0498-0.02140.3632-0.07450.2533-79.734455.8111-0.3872
131.8914-0.44570.11614.80860.72924.8958-0.1581-0.19210.21070.12490.02330.0379-0.1208-0.00030.08840.26350.0462-0.08310.2912-0.03640.257-62.467370.932216.7736
142.96840.08270.41984.12940.76396.5422-0.27290.41590.5707-0.30190.19670.2374-1.07290.409-0.10740.4767-0.1035-0.05260.33910.13840.3422-16.566835.5444-16.8477
151.9467-0.6711-0.97853.9727-0.5995.7825-0.2572-0.29050.37290.0539-0.03890.0596-1.0349-0.61490.20650.60220.0954-0.17020.4792-0.15850.4079-61.5158-2.245719.1936
165.1311-0.2217-5.0029.2795-0.71315.2143-0.53111.2194-0.3254-0.97810.20190.20821.1069-1.53350.52660.73240.0137-0.03550.60390.05380.5283-43.29060.936922.2246
173.76551.26224.31143.94930.74338.58920.44970.7304-0.33970.18220.0351-0.8867-0.07631.117-0.50470.5789-0.18910.00550.80410.19091.7-30.6379-31.7047-20.5309
189.5092-5.08891.27513.0361-2.11596.6920.4173-0.7646-0.88120.18440.59760.57070.28711.0415-0.62160.61250.05020.00290.6068-0.20270.5537-36.122235.211-20.7457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )A1 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 213 )A114 - 213
3X-RAY DIFFRACTION3chain 'E' and (resid 1 through 113 )E1 - 113
4X-RAY DIFFRACTION4chain 'E' and (resid 114 through 213 )E114 - 213
5X-RAY DIFFRACTION5chain 'F' and (resid 1 through 107 )F1 - 107
6X-RAY DIFFRACTION6chain 'F' and (resid 108 through 213 )F108 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 107 )B1 - 107
8X-RAY DIFFRACTION8chain 'B' and (resid 108 through 212 )B108 - 212
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 113 )I1 - 113
10X-RAY DIFFRACTION10chain 'I' and (resid 114 through 213 )I114 - 213
11X-RAY DIFFRACTION11chain 'J' and (resid 1 through 107 )J1 - 107
12X-RAY DIFFRACTION12chain 'J' and (resid 108 through 213 )J108 - 213
13X-RAY DIFFRACTION13chain 'K' and (resid 2 through 112 )K2 - 112
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 112 )C2 - 112
15X-RAY DIFFRACTION15chain 'G' and (resid 2 through 112 )G2 - 112
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 12 )D2 - 12
17X-RAY DIFFRACTION17chain 'H' and (resid 4 through 11 )H4 - 11
18X-RAY DIFFRACTION18chain 'L' and (resid 2 through 11 )L2 - 11

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