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- PDB-6axl: Crystal structure of Fab317 complex -

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Basic information

Entry
Database: PDB / ID: 6axl
TitleCrystal structure of Fab317 complex
Components
  • Fab317 heavy chain
  • Fab317 light chains
  • Peptide ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-NH2
KeywordsIMMUNE SYSTEM / Fab fragment
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: 2.4 Å
AuthorsOyen, D. / Wilson, I.A.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural basis for antibody recognition of the NANP repeats in circumsporozoite protein.
Authors: David Oyen / Jonathan L Torres / Ulrike Wille-Reece / Christian F Ockenhouse / Daniel Emerling / Jacob Glanville / Wayne Volkmuth / Yevel Flores-Garcia / Fidel Zavala / Andrew B Ward / C ...Authors: David Oyen / Jonathan L Torres / Ulrike Wille-Reece / Christian F Ockenhouse / Daniel Emerling / Jacob Glanville / Wayne Volkmuth / Yevel Flores-Garcia / Fidel Zavala / Andrew B Ward / C Richter King / Ian A Wilson /
Abstract: Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)- ...Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)-based vaccine against that contains 19 NANP repeats followed by a thrombospondin repeat domain. Although RTS,S has undergone extensive clinical testing and has progressed through phase III clinical trials, continued efforts are underway to enhance its efficacy and duration of protection. Here, we determined that two monoclonal antibodies (mAbs 311 and 317), isolated from a recent controlled human malaria infection trial exploring a delayed fractional dose, inhibit parasite development in vivo by at least 97%. Crystal structures of antibody fragments (Fabs) 311 and 317 with an (NPNA) peptide illustrate their different binding modes. Notwithstanding, one and three of the three NPNA repeats adopt similar well-defined type I β-turns with Fab311 and Fab317, respectively. Furthermore, to explore antibody binding in the context of CSP, we used negative-stain electron microscopy on a recombinant shortened CSP (rsCSP) construct saturated with Fabs. Both complexes display a compact rsCSP with multiple Fabs bound, with the rsCSP-Fab311 complex forming a highly organized helical structure. Together, these structural insights may aid in the design of a next-generation malaria vaccine.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 1.4Oct 23, 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
C: Fab317 light chains
D: Fab317 heavy chain
B: Fab317 light chains
A: Fab317 heavy chain
G: Peptide ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-NH2
I: Peptide ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-NH2


Theoretical massNumber of molelcules
Total (without water)97,1426
Polymers97,1426
Non-polymers00
Water8,737485
1
B: Fab317 light chains
A: Fab317 heavy chain
G: Peptide ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-NH2


Theoretical massNumber of molelcules
Total (without water)48,5713
Polymers48,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-25 kcal/mol
Surface area20380 Å2
MethodPISA
2
C: Fab317 light chains
D: Fab317 heavy chain
I: Peptide ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-NH2


Theoretical massNumber of molelcules
Total (without water)48,5713
Polymers48,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-24 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.663, 65.342, 99.043
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab317 light chains


Mass: 23408.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab317 heavy chain


Mass: 23930.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Peptide ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-NH2


Mass: 1231.255 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium Citrate pH4.0 1M Lithium Chloride 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→40.93 Å / Num. obs: 38939 / % possible obs: 97.8 % / Redundancy: 6.1 % / CC1/2: 0.92 / Rpim(I) all: 0.079 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.44 Å / CC1/2: 0.732 / Rpim(I) all: 0.43

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2.4→40.93 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.87
RfactorNum. reflection% reflection
Rfree0.217 1883 4.84 %
Rwork0.175 --
obs0.178 38916 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 0 485 7188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026871
X-RAY DIFFRACTIONf_angle_d0.5919359
X-RAY DIFFRACTIONf_dihedral_angle_d19.1674089
X-RAY DIFFRACTIONf_chiral_restr0.0451044
X-RAY DIFFRACTIONf_plane_restr0.0031210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4006-2.46550.27891330.24332719X-RAY DIFFRACTION94
2.4655-2.5380.30381400.23652877X-RAY DIFFRACTION99
2.538-2.61990.30731420.22422853X-RAY DIFFRACTION98
2.6199-2.71360.27221270.21372868X-RAY DIFFRACTION98
2.7136-2.82220.23651350.20682771X-RAY DIFFRACTION95
2.8222-2.95060.24281380.20152840X-RAY DIFFRACTION98
2.9506-3.10610.23891580.19762859X-RAY DIFFRACTION98
3.1061-3.30060.22631450.18022863X-RAY DIFFRACTION98
3.3006-3.55530.22041540.16372860X-RAY DIFFRACTION98
3.5553-3.91290.22191520.15942817X-RAY DIFFRACTION97
3.9129-4.47850.18321520.13022870X-RAY DIFFRACTION99
4.4785-5.64010.15621680.13172853X-RAY DIFFRACTION97
5.6401-40.93450.19721390.18462983X-RAY DIFFRACTION98
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)
17.7084-2.75221.11993.92540.84525.0201-0.2895-0.96040.16620.57950.3307-0.0392-0.147-0.2368-0.01070.2838-0.01790.00630.2935-0.02210.2408-17.087826.9275-30.1719
24.4314-1.359-0.03293.3432-0.56772.2625-0.10850.08780.29880.17860.00940.07560.0011-0.07870.14350.2080.0020.01390.1799-0.01090.2622-13.098221.9875-39.2128
34.9537-2.3975-0.31053.316-0.72931.44670.1868-0.01390.2996-0.0472-0.0752-0.111-0.27730.0122-0.0590.2149-0.01-0.00720.1876-0.02680.1926-13.457722.7945-36.0096
40.4204-0.2941-1.3590.25891.06084.493-0.4598-0.38770.04320.26120.30760.1028-0.463-0.09380.08310.350.12980.11650.335-0.01640.5004-34.022429.6997-27.4416
54.22760.75320.38597.0311-2.60944.9253-0.1734-0.15050.15091.05060.25441.48530.2461-0.7525-0.13710.3654-0.07260.11270.4307-0.21140.5219-48.82988.6724-12.2692
61.01610.5265-0.32943.7566-1.83433.12710.2197-0.15350.19740.2141-0.19810.03650.0543-0.29150.05560.2982-0.02380.02660.4154-0.01180.3936-38.709217.9964-12.0448
72.43031.9904-1.36465.1626-1.96453.44510.3061-0.35710.2290.4122-0.43160.4209-0.0344-0.0716-0.00750.2025-0.03040.06510.4276-0.11340.3661-43.184718.2432-12.0371
82.95741.3376-2.24521.5685-0.96448.1083-0.42220.1239-0.2826-0.26460.0283-0.16260.6835-0.18140.37790.1823-0.00080.02220.1456-0.00570.2906-17.4665-1.9915-41.0073
93.1872-0.694-1.00433.9336-0.83544.0764-0.032-0.05910.04720.03950.0979-0.1217-0.02750.1852-0.07150.0872-0.00370.00320.1428-0.00980.1684-8.98011.3391-35.6138
103.5221-0.4978-1.7013.5909-1.48164.5064-0.201-0.3321-0.10310.4002-0.0014-0.08710.13320.30440.25430.1850.0061-0.00550.18690.01120.2738-14.8717-3.9133-30.8559
114.06151.9386-1.7761.2366-0.73711.3296-0.004-0.02550.0307-0.00180.04010.01570.0474-0.00710.01520.20810.04520.02110.18770.00640.1941-19.0394.3932-35.6658
123.4583-0.33780.7147.9642-2.07994.1408-0.2621-0.16040.36050.62430.4090.6756-0.4579-0.4197-0.07590.29020.06450.00030.3892-0.03170.3667-48.13658.8958-19.5332
133.1376-0.34210.17325.0558-0.66823.3254-0.0427-0.00060.4299-0.213-0.10160.0556-0.1917-0.41640.13580.22830.005-0.02030.29140.03090.2595-42.93319.0631-25.5458
147.2356-4.774-2.04813.51061.25584.5622-0.1106-0.32440.1924-0.28150.2650.4881-0.2261-0.1859-0.24160.2302-0.0008-0.0740.3444-0.00750.4989-51.15853.5606-27.2241
152.0576-1.75910.5217.4627-2.77664.2527-0.19190.1563-0.204-0.52720.29710.08590.4828-0.2606-0.0230.3302-0.18670.04270.3422-0.06650.3449-0.795110.7626-79.1194
162.7146-0.25191.0552.1851-1.10592.842-0.10820.1603-0.1948-0.24640.20140.15630.151-0.1809-0.09490.2231-0.08980.02040.2617-0.02810.2495-1.525412.7009-69.9838
170.33420.5407-1.37840.7881-2.13915.75150.24020.2084-0.01320.23410.05850.0713-0.3478-0.1605-0.26190.3325-0.06320.06380.39810.00280.27730.149821.7662-92.3147
187.4470.31781.43682.87721.17445.0182-0.05630.11350.9155-0.3592-0.0429-0.2-0.47620.65910.03460.348-0.07060.01910.29140.05620.323927.09432.0381-100.0026
192.8041-0.8629-2.24040.34670.76642.0438-0.05610.1386-0.42340.0312-0.1438-0.15670.2677-0.06890.23970.3589-0.0166-0.03250.17970.04660.330616.060522.1713-98.2913
207.4078-0.047-1.47731.2189-0.01112.75950.15030.2376-0.1739-0.0645-0.15170.01830.07050.1019-0.00250.3207-0.0226-0.02540.1043-0.00430.228720.169623.0797-100.8761
213.11270.878-1.2241.2816-0.13692.7020.315-0.24770.5473-0.1887-0.0785-0.099-0.27680.0187-0.24610.2793-0.05560.01080.177-0.04630.30221.720924.7352-62.6046
226.01390.2567-4.50313.00160.4453.42750.5899-0.30930.71050.5069-0.10940.1531-0.48330.1855-0.38310.3487-0.05060.03280.2761-0.01620.284212.510723.4852-52.8382
235.31811.61770.90355.7309-3.14945.22580.02610.54610.455-0.32880.2885-0.07270.4850.5453-0.18560.1585-0.0421-0.0050.2069-0.01720.277114.099616.5306-67.2612
245.2292-0.6177-2.32731.6898-1.13854.5498-0.2009-0.1821-0.50050.1281-0.0877-0.33890.4120.17580.19180.1547-0.01740.01880.14040.01540.284717.206912.7007-54.5257
255.501-0.5319-1.55961.8123-0.45952.9208-0.25750.3579-0.79140.4034-0.1640.16030.638-0.06910.47250.1969-0.08260.03420.2048-0.03320.335823.694917.3816-61.5564
261.41820.927-0.97691.5959-1.03531.6144-0.15790.130.02630.05610.037-0.0524-0.1291-0.04190.02950.2039-0.0466-0.02750.2181-0.00560.270314.666621.2775-65.3003
273.7258-1.0733-1.69653.55460.15840.8770.08670.6291-0.0429-0.5255-0.0472-0.1938-0.18940.0840.00140.4184-0.1069-0.0310.28510.0650.303921.874936.9443-100.7904
282.4272-0.94221.72961.6309-2.46424.9992-0.1274-0.00440.098-0.0033-0.1268-0.2471-0.1223-0.11660.21280.2888-0.042-0.00880.15770.00710.301121.381935.5496-87.3851
295.3036-1.02832.22934.6823-1.17744.56130.1367-0.00030.1881-0.066-0.14240.2479-0.0282-0.19220.02770.2265-0.0280.00340.1963-0.00690.226417.887732.7989-90.5282
302.7668-0.24210.91053.6469-1.10434.49-0.31430.14440.35690.00560.14710.0365-0.78880.18010.13680.4475-0.0805-0.10720.16720.0090.393823.172842.9499-90.138
313.434-3.47311.4834.4103-2.97893.1281-0.37410.07720.3838-0.20170.2771-0.755-0.2125-0.23850.02640.276-0.04990.01740.3456-0.03120.2653-1.822918.2548-46.5816
324.26395.1599-1.10426.2803-1.12482.00790.2225-0.0378-0.76890.5583-0.3673-0.9675-0.25360.3466-0.01710.30570.0295-0.0480.21750.02490.31541.85289.0067-42.6691
336.4385-0.53345.23345.3916-3.62686.15580.0888-0.93860.05530.8786-0.06470.9423-0.6698-0.2027-0.34020.32750.04380.02750.30520.04930.3442-4.49129.0492-55.5918
343.83324.37613.3345.31044.16823.3292-0.03570.1907-0.74690.7622-0.449-0.41890.58750.46060.24430.2689-0.0890.03480.30240.07370.36134.9866.5145-51.1769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'C' AND (RESID 1 THROUGH 18 )
2X-RAY DIFFRACTION2CHAIN 'C' AND (RESID 19 THROUGH 61 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 62 THROUGH 102 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 103 THROUGH 113 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 114 THROUGH 128 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 129 THROUGH 163 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 164 THROUGH 213 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 1 THROUGH 33 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 34 THROUGH 75 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 76 THROUGH 87 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 88 THROUGH 119 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 120 THROUGH 145 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 146 THROUGH 188 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 189 THROUGH 213 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 1 THROUGH 18 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 19 THROUGH 102 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 103 THROUGH 113 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 114 THROUGH 128 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 129 THROUGH 150 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 151 THROUGH 213 )
21X-RAY DIFFRACTION21CHAIN 'A' AND (RESID 1 THROUGH 17 )
22X-RAY DIFFRACTION22CHAIN 'A' AND (RESID 18 THROUGH 33 )
23X-RAY DIFFRACTION23CHAIN 'A' AND (RESID 34 THROUGH 45 )
24X-RAY DIFFRACTION24CHAIN 'A' AND (RESID 46 THROUGH 75 )
25X-RAY DIFFRACTION25CHAIN 'A' AND (RESID 76 THROUGH 87 )
26X-RAY DIFFRACTION26CHAIN 'A' AND (RESID 88 THROUGH 119 )
27X-RAY DIFFRACTION27CHAIN 'A' AND (RESID 120 THROUGH 134 )
28X-RAY DIFFRACTION28CHAIN 'A' AND (RESID 135 THROUGH 157 )
29X-RAY DIFFRACTION29CHAIN 'A' AND (RESID 158 THROUGH 188 )
30X-RAY DIFFRACTION30CHAIN 'A' AND (RESID 189 THROUGH 214 )
31X-RAY DIFFRACTION31CHAIN 'G' AND (RESID 2 THROUGH 6 )
32X-RAY DIFFRACTION32CHAIN 'G' AND (RESID 7 THROUGH 14 )
33X-RAY DIFFRACTION33CHAIN 'I' AND (RESID 2 THROUGH 6 )
34X-RAY DIFFRACTION34CHAIN 'I' AND (RESID 7 THROUGH 14 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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