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- PDB-6azm: Crystal structure of the 580 germline antibody bound to circumspo... -

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Basic information

Entry
Database: PDB / ID: 6azm
TitleCrystal structure of the 580 germline antibody bound to circumsporozoite protein NANP 5-mer
Components
  • 580 germline antibody, heavy chain
  • 580 germline antibody, light chain
  • Circumsporozoite protein NANP 5-mer
KeywordsIMMUNE SYSTEM / Malaria / Circumsporozoite protein / Fab
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsScally, S.W. / Bosch, A. / Triller, G. / Wardemann, H. / Julien, J.P.
CitationJournal: Immunity / Year: 2017
Title: Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies.
Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, ...Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, A.A. / Mordmuller, B. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionSep 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Apr 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 580 germline antibody, light chain
B: 580 germline antibody, heavy chain
C: 580 germline antibody, light chain
D: 580 germline antibody, heavy chain
F: Circumsporozoite protein NANP 5-mer
E: Circumsporozoite protein NANP 5-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3867
Polymers99,2946
Non-polymers921
Water18,4651025
1
A: 580 germline antibody, light chain
B: 580 germline antibody, heavy chain
E: Circumsporozoite protein NANP 5-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7394
Polymers49,6473
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 580 germline antibody, light chain
D: 580 germline antibody, heavy chain
F: Circumsporozoite protein NANP 5-mer


Theoretical massNumber of molelcules
Total (without water)49,6473
Polymers49,6473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.961, 166.555, 72.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 580 germline antibody, light chain


Mass: 24168.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment: Fab / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 580 germline antibody, heavy chain


Mass: 23478.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment: Fab / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein NANP 5-mer


Mass: 2000.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Circumsporozoite protein NANP 5-mer
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1025 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% Isopropanol, 100mM HEPES pH 7.5, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 113396 / % possible obs: 98.8 % / Redundancy: 4.3 % / Rpim(I) all: 0.046 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 18628 / Rpim(I) all: 0.397 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SHELXPREPdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 580 Fab Crystal structure

Resolution: 1.6→37.511 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1993 2005 1.77 %
Rwork0.1662 --
obs0.1668 113328 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→37.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6814 0 6 1025 7845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066993
X-RAY DIFFRACTIONf_angle_d0.8629527
X-RAY DIFFRACTIONf_dihedral_angle_d13.7024188
X-RAY DIFFRACTIONf_chiral_restr0.0551064
X-RAY DIFFRACTIONf_plane_restr0.0051228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2871380.257843X-RAY DIFFRACTION98
1.64-1.68440.2761420.23997831X-RAY DIFFRACTION99
1.6844-1.73390.25071450.22617905X-RAY DIFFRACTION99
1.7339-1.78990.23841390.20827893X-RAY DIFFRACTION99
1.7899-1.85390.25811430.19687894X-RAY DIFFRACTION99
1.8539-1.92810.20471460.17897939X-RAY DIFFRACTION99
1.9281-2.01580.19471440.16917935X-RAY DIFFRACTION99
2.0158-2.12210.22481410.16497985X-RAY DIFFRACTION99
2.1221-2.2550.18751420.16397972X-RAY DIFFRACTION99
2.255-2.42910.19271450.16577979X-RAY DIFFRACTION99
2.4291-2.67350.19251480.1698004X-RAY DIFFRACTION99
2.6735-3.06020.20431440.16367986X-RAY DIFFRACTION99
3.0602-3.85490.18361410.14448015X-RAY DIFFRACTION98
3.8549-37.52120.16691470.14198142X-RAY DIFFRACTION96
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)
10.630.3760.18062.15811.27881.2231-0.07430.03410.0115-0.08050.03710.0983-0.0237-0.0650.04730.1152-0.0075-0.00730.09040.0040.0866-15.8941-31.82264.0328
22.9798-1.02491.73460.9828-0.25571.64260.0803-0.0981-0.09060.1840.0719-0.09950.16280.0703-0.09230.18770.0334-0.03680.1446-0.01140.10761.0091-26.329933.5001
32.7504-0.81592.38621.0645-0.85783.8035-0.1097-0.07940.08360.37950.0909-0.1563-0.15280.24940.10740.23110.0422-0.05360.2145-0.03970.15477.219-22.752639.5044
43.66510.32491.69491.2770.62871.89720.0368-0.2371-0.09250.5414-0.0511-0.07140.1987-0.09950.00670.2931-0.01720.0030.11320.01910.1338-14.6577-55.606213.7913
51.4214-0.08030.84462.06140.12791.1991-0.03810.0405-0.07280.23430.0369-0.13480.06950.0785-0.0010.1474-0.0087-0.00040.1105-0.01180.1048-10.5147-52.70086.9895
61.5284-0.6170.20951.10560.04921.29640.0533-0.3986-0.1190.47830.2115-0.10420.36090.05-0.22780.3522-0.0089-0.13420.24960.02850.2287-0.7288-37.402337.6883
72.2852-1.93550.05713.65420.74251.99350.081-0.2268-0.37890.28990.14050.38520.5942-0.2746-0.13920.3274-0.039-0.06270.23950.07570.2335-6.9931-38.057637.4699
84.7394-3.5512-1.28865.18021.28172.38940.0165-0.0478-0.01140.19850.05580.09810.0379-0.0177-0.04460.0882-0.01160.01280.09130.01350.1137-12.6189-14.69414.2151
92.881-0.03590.53061.49530.83961.143-0.16910.1250.0177-0.2056-0.23110.9739-0.1157-0.4432-0.84350.03550.0096-0.12160.2052-0.03960.5731-29.3081-4.3141-1.8373
103.6238-0.02430.79343.7350.0482.82590.00950.02990.0467-0.04790.0032-0.2101-0.10940.3034-0.03090.0655-0.00290.00290.11960.00330.1103-7.7126-4.4438-2.2406
114.0529-1.96910.35363.70840.28511.45690.13970.2464-0.0911-0.2937-0.17970.21880.06640.00620.05470.10660.006-0.03050.1096-0.00430.1259-16.0385-10.7718-6.8801
122.6485-2.43240.21632.6854-0.18070.2037-0.0540.0173-0.01740.06510.06240.02880.0154-0.0038-0.00610.0715-0.01030.00050.0989-0.00520.1109-7.3309-10.90532.1134
132.39981.21751.4042.29761.32493.6401-0.15550.04010.3212-0.18520.1423-0.3066-0.36240.3227-0.00610.1409-0.0324-0.05820.2649-0.09250.348427.1663-6.358517.4648
143.04392.01792.91921.85932.73964.7323-0.0227-0.32560.05980.080.0031-0.06280.0713-0.0278-0.00080.09230.0415-0.03630.172-0.03680.172315.226-15.804516.559
152.96550.38683.43782.40571.52036.4701-0.1751-0.11140.0286-0.14560.03640.0719-0.3943-0.01360.15550.0415-0.01560.0190.1306-0.00410.136612.5775-13.833614.2906
161.52260.93812.13882.4640.63883.3619-0.0562-0.43020.07140.16840.0329-0.3056-0.070.15090.00470.15860.0368-0.06540.3664-0.09990.239423.4638-11.317524.8937
176.34894.15663.07623.60261.69192.63350.10660.075-0.26550.17350.1508-0.36630.32970.3749-0.20290.18260.0907-0.03560.2321-0.0530.234622.492-21.723818.3785
182.0525-0.39721.80830.8437-0.41864.4563-0.01110.16950.0688-0.0559-0.0257-0.3687-0.29110.38660.0130.1131-0.02660.00130.12020.02850.2089-5.100814.5813-0.7733
191.5159-0.53230.96791.91720.05781.6552-0.012-0.04280.09060.09110.0231-0.1258-0.16270.0219-0.01790.0984-0.00510.00340.11170.010.1301-11.367511.41383.8414
201.31780.77970.66230.92910.90871.2298-0.19210.09360.02980.04030.4358-0.50510.00810.307-0.20790.196-0.0546-0.00860.2428-0.06760.268920.384-1.891113.4055
212.7735-1.3562-0.33173.54831.24091.3175-0.00840.18710.1559-0.61840.1418-0.339-0.42260.2116-0.13840.2225-0.05750.03020.1827-0.02830.212217.9968-3.5128.1272
222.8258-1.1034-1.60820.46530.86372.6573-0.13640.3646-0.01-0.66740.1708-1.0048-0.26210.1995-0.24230.4144-0.14220.20380.2954-0.05040.592424.37582.40524.0286
237.3171-0.18786.38558.236-1.23416.56990.25490.52180.2693-0.4820.02660.8487-0.3232-0.8417-0.31080.18240.049-0.08430.20780.04390.3079-27.62574.7368-6.0107
241.1347-0.1489-1.00096.9345-1.36082.2836-0.42440.8871-0.635-0.71040.30440.41330.2125-0.51270.26060.2097-0.0696-0.03640.2119-0.02610.1897-21.3509-47.7703-9.2143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 213 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 33 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 134 )
7X-RAY DIFFRACTION7chain 'B' and (resid 135 through 213 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 25 )
9X-RAY DIFFRACTION9chain 'C' and (resid 26 through 32 )
10X-RAY DIFFRACTION10chain 'C' and (resid 33 through 48 )
11X-RAY DIFFRACTION11chain 'C' and (resid 49 through 75 )
12X-RAY DIFFRACTION12chain 'C' and (resid 76 through 113 )
13X-RAY DIFFRACTION13chain 'C' and (resid 114 through 128 )
14X-RAY DIFFRACTION14chain 'C' and (resid 129 through 150 )
15X-RAY DIFFRACTION15chain 'C' and (resid 151 through 174 )
16X-RAY DIFFRACTION16chain 'C' and (resid 175 through 197 )
17X-RAY DIFFRACTION17chain 'C' and (resid 198 through 213 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 33 )
19X-RAY DIFFRACTION19chain 'D' and (resid 34 through 109 )
20X-RAY DIFFRACTION20chain 'D' and (resid 110 through 134 )
21X-RAY DIFFRACTION21chain 'D' and (resid 135 through 189 )
22X-RAY DIFFRACTION22chain 'D' and (resid 190 through 213 )
23X-RAY DIFFRACTION23chain 'F' and (resid 2 through 9 )
24X-RAY DIFFRACTION24chain 'E' and (resid 2 through 9 )

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