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- PDB-6uud: Crystal structure of antibody 5D5 in complex with PfCSP N-termina... -

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Basic information

Entry
Database: PDB / ID: 6uud
TitleCrystal structure of antibody 5D5 in complex with PfCSP N-terminal peptide
Components
  • (5D5 Antibody Fab, ...) x 2
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / Antibody
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 speciesMus musculus (house mouse)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsThai, E. / Scally, S.W. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906; J.-P.J. United States
CitationJournal: J.Exp.Med. / Year: 2020
Title: A high-affinity antibody against the CSP N-terminal domain lacks Plasmodium falciparum inhibitory activity.
Authors: Thai, E. / Costa, G. / Weyrich, A. / Murugan, R. / Oyen, D. / Flores-Garcia, Y. / Prieto, K. / Bosch, A. / Valleriani, A. / Wu, N.C. / Pholcharee, T. / Scally, S.W. / Wilson, I.A. / ...Authors: Thai, E. / Costa, G. / Weyrich, A. / Murugan, R. / Oyen, D. / Flores-Garcia, Y. / Prieto, K. / Bosch, A. / Valleriani, A. / Wu, N.C. / Pholcharee, T. / Scally, S.W. / Wilson, I.A. / Wardemann, H. / Julien, J.P. / Levashina, E.A.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 27, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Apr 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 5D5 Antibody Fab, heavy chain
L: 5D5 Antibody Fab, light chain
A: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9285
Polymers49,2953
Non-polymers6332
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-3 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.601, 60.901, 72.435
Angle α, β, γ (deg.)90.000, 97.666, 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

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody 5D5 Antibody Fab, heavy chain


Mass: 23468.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 5D5 Antibody Fab, light chain


Mass: 23631.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein/peptide / Sugars , 2 types, 2 molecules A

#3: Protein/peptide Circumsporozoite protein


Mass: 2195.604 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 417 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M di-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 38412 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.7
Reflection shellResolution: 1.85→1.95 Å / Num. unique obs: 5588 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal

Resolution: 1.85→39.74 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1855
RfactorNum. reflection% reflection
Rfree0.2235 1920 5 %
Rwork0.1781 --
obs0.1804 38396 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 42 416 3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543534
X-RAY DIFFRACTIONf_angle_d0.79134809
X-RAY DIFFRACTIONf_chiral_restr0.0529549
X-RAY DIFFRACTIONf_plane_restr0.005609
X-RAY DIFFRACTIONf_dihedral_angle_d13.34542126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.32511370.27612606X-RAY DIFFRACTION98.78
1.9-1.950.29411350.23792577X-RAY DIFFRACTION98.69
1.95-20.28241350.21712562X-RAY DIFFRACTION98.32
2-2.070.27941380.22042596X-RAY DIFFRACTION98.17
2.07-2.140.29791350.21612560X-RAY DIFFRACTION98.43
2.14-2.230.26011340.21272569X-RAY DIFFRACTION98.04
2.23-2.330.31951370.20342603X-RAY DIFFRACTION98.42
2.33-2.450.24971380.20382609X-RAY DIFFRACTION98.99
2.45-2.610.24641360.20642582X-RAY DIFFRACTION98.26
2.61-2.810.24831370.19852610X-RAY DIFFRACTION98.81
2.81-3.090.22711380.18012626X-RAY DIFFRACTION99.28
3.09-3.540.20021390.1592631X-RAY DIFFRACTION99.28
3.54-4.460.15931390.13862646X-RAY DIFFRACTION99.11
4.46-39.740.19081420.14692699X-RAY DIFFRACTION99.37
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)
13.08456076787-2.299201573812.476406923894.63408830023-3.592646057715.165978088430.00637556311745-0.327820825993-0.249941580376-0.0591791586710.2618011633750.2482726438380.393886654715-0.0549921665787-0.2883976264390.2818315405030.01551278707960.0753057552920.2307747186060.02445186093610.211365482679-22.7447009659-14.5023058869-6.48423418872
28.01193231322-1.09015617410.2549331252678.6538542456-1.133815371954.868434410770.01312514531020.3982893053280.0400823745074-0.06261736974620.315515657244-0.132784894056-0.4212034550610.384289258197-0.2142265533090.184201736502-0.01907074595640.02113133469180.263607505334-0.04459022261050.161357366131-13.5690719658-6.98932892672-7.98168255389
33.03445819803-1.012599007341.61097739161.11562457486-0.7116166915775.23024225743-0.22400556752-0.4698180308130.165206589430.4904248000570.3737492910040.16191240267-0.6189181992670.0116391684566-0.02259135459510.319992146150.04987687537460.05269243508610.272702384671-0.05024135902570.208243790369-20.5661516402-5.33746924757-1.52763293932
42.96864886254-0.3324110794471.035979405052.44607148131-0.2964599006815.390694037230.0556727767884-0.104385149632-0.3100020214790.1955354596990.13702008124-0.09739463884520.3705335352420.827752760341-0.1864956905590.3023763206660.07971612414480.01854740068930.337275750543-0.0227886511340.205699983082-11.8195554461-14.8015027615-7.35956310605
51.07923731882-0.360190347001-0.4888062457553.676738653421.671776726861.738324420540.02473107317040.0317776525473-0.0440226659382-0.0813023609419-0.03409648322530.126890346652-0.0573239558102-0.1656322203340.007843639695540.1501163293340.01812570897440.008101793708660.1465142921070.02555053924490.160364908392-27.5292922245-18.0190333327-32.5401991134
61.857277820370.6513220143081.16737673752.484626441930.1554149809460.771534772441-0.02231313906970.121774780186-0.3280528429830.1385472973760.08896669125280.4685666800210.331703864949-0.320112967485-0.03666111846930.237892291382-0.03387189259930.0138024622090.256581529167-0.0002194587424140.355089439309-35.0462072629-24.1544440853-32.8541738256
73.31431149228-0.9718845201880.2244030527575.691320092393.560734592916.898454640160.033866133822-0.2639946509420.4167930509960.08513331645280.0241845862604-0.523700567056-0.4170912675520.795229976202-0.04673027740040.231894463886-0.1166830485010.03656254875320.376071774339-0.00948573826390.2952653903953.79468234691-7.62451704838-21.5618834678
83.079130528760.02753333796750.6950240363193.106552038891.772171511965.22104901822-0.0979431576493-0.5711986110730.00708499408550.3189444446350.0903520227606-0.2432036056640.1990473651580.579771791001-0.008057227437830.1942843770650.004222278893780.006908734443680.3992603146080.02093993704790.1902875814630.564502162132-13.9730023444-14.0409094549
90.4450308317741.3574249141.938034974983.814384590345.313528931878.52334763217-0.09576978484570.1252524294830.00752573168253-0.117957735880.0996053533926-0.117912684115-0.0265487579430.5263679800670.002626924705350.1860654414880.03536085767250.02832865023850.219142732403-0.02455113003710.249151586291-3.55213031216-14.6656401453-36.8767065183
103.95515004132-0.768520377589-0.4442698859842.43853307133-0.2049901646722.59108165339-0.002218389445020.184847976754-0.157554675691-0.07029139105610.0237143843120.4045893877430.0752819939596-0.418724358549-0.05122713659260.209418053997-0.0133937572214-0.04122546865310.227934190808-0.009853018232730.23169985977-33.8261233228-16.8818426096-43.5668937414
115.76545763146-1.366907000820.2635162530872.2476240781-0.4287881838621.667980621330.001117413269280.07495234881470.271634759977-0.0860548806010.00727632928365-0.116689347269-0.07113780936190.120786240403-0.0002892867532280.2134045518050.0135102813024-0.009095634786950.170326277418-0.01354999849160.173103662476-19.1379510587-11.3636255221-45.3908398589
127.64987034304-4.340203631064.433984913893.7360026756-2.474821257685.06569655931-0.04835165490030.07985951824060.0171259068945-0.02989253286210.06974163959910.0530163007995-0.03302817822160.122442046037-0.06584490501880.157734284825-0.04704921573510.02863924992020.128223788994-0.02434023323430.192689173849-18.0057865309-11.163829591-41.6173884584
134.05402718678-0.516406376003-0.6768457097591.167017923460.3781369368352.304653312280.06786896016970.6792385253810.0995187878583-0.272852855816-0.03505029937290.1007719238230.0230156213266-0.357031267316-0.06616962534570.281092876287-0.00549443148113-0.01195635460690.2280115310010.04070462774480.185488206951-26.8706282227-11.8951593634-51.3476910884
148.668820754283.46683617384.332572467556.952951175624.782937311293.84584759141-0.179045268266-1.048505817730.1070813568480.5738669902030.304486977095-0.324355637943-0.500141842920.877496484417-0.09194176070130.4619579470010.03716066449230.002287352522580.719788338572-0.1021324829460.287617190614-5.71132358571-11.39253935786.66580380695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'H' and (resid 33 through 52 )
3X-RAY DIFFRACTION3chain 'H' and (resid 52A through 87 )
4X-RAY DIFFRACTION4chain 'H' and (resid 88 through 106 )
5X-RAY DIFFRACTION5chain 'H' and (resid 107 through 203 )
6X-RAY DIFFRACTION6chain 'H' and (resid 204 through 215 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 25 )
8X-RAY DIFFRACTION8chain 'L' and (resid 26 through 101 )
9X-RAY DIFFRACTION9chain 'L' and (resid 102 through 113 )
10X-RAY DIFFRACTION10chain 'L' and (resid 114 through 128 )
11X-RAY DIFFRACTION11chain 'L' and (resid 129 through 150 )
12X-RAY DIFFRACTION12chain 'L' and (resid 151 through 174 )
13X-RAY DIFFRACTION13chain 'L' and (resid 175 through 213 )
14X-RAY DIFFRACTION14chain 'A' and (resid 81 through 92 )

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