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- PDB-6ulf: Crystal structure of 4498 Fab in complex with circumsporozoite pr... -

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Basic information

Entry
Database: PDB / ID: 6ulf
TitleCrystal structure of 4498 Fab in complex with circumsporozoite protein NDN3 and anti-Kappa VHH domain
Components
  • 4498 Fab heavy chain
  • 4498 Fab light chain
  • Circumsporozoite protein
  • anti Kappa VHH domain
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 speciesHomo sapiens (human)
Camelidae mixed library (mammal)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsThai, E. / Scally, S.W. / Prieto, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906; J.-P.J. 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
DepositionOct 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 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 1.3Oct 11, 2023Group: 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4498 Fab heavy chain
B: 4498 Fab light chain
K: anti Kappa VHH domain
P: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)60,6844
Polymers60,6844
Non-polymers00
Water11,440635
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-37 kcal/mol
Surface area25020 Å2
Unit cell
Length a, b, c (Å)61.536, 76.084, 63.247
Angle α, β, γ (deg.)90.000, 98.321, 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

#1: Antibody 4498 Fab heavy chain


Mass: 24749.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 4498 Fab light chain


Mass: 23371.967 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Source: (synth.) Camelidae mixed library (mammal)
#4: Protein/peptide Circumsporozoite protein / CS


Mass: 1236.248 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M phosphate-citrate pH 4.2, 20 % (w/v) PEG 8000, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 62305 / % possible obs: 98.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 3120 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D01

6d01


Resolution: 1.7→38.04 Å / SU ML: 0.1804 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.6205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 2003 3.22 %
Rwork0.2074 60263 -
obs0.2083 62266 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 0 635 4799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00574264
X-RAY DIFFRACTIONf_angle_d0.87285824
X-RAY DIFFRACTIONf_chiral_restr0.0604663
X-RAY DIFFRACTIONf_plane_restr0.0055757
X-RAY DIFFRACTIONf_dihedral_angle_d16.52841444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.31611450.25914223X-RAY DIFFRACTION96.72
1.74-1.790.2281330.24594214X-RAY DIFFRACTION96.82
1.79-1.840.29771410.23444255X-RAY DIFFRACTION97.21
1.84-1.90.30731390.22714268X-RAY DIFFRACTION97.44
1.9-1.970.23671430.20984240X-RAY DIFFRACTION97.4
1.97-2.050.24531380.21074300X-RAY DIFFRACTION97.69
2.05-2.140.2361420.20484278X-RAY DIFFRACTION97.92
2.14-2.250.23161450.20494312X-RAY DIFFRACTION98.19
2.25-2.40.22291480.21214287X-RAY DIFFRACTION98.45
2.4-2.580.24481440.21924352X-RAY DIFFRACTION98.68
2.58-2.840.23911420.21124331X-RAY DIFFRACTION98.81
2.84-3.250.22891440.20244370X-RAY DIFFRACTION98.93
3.25-4.090.1881470.18834370X-RAY DIFFRACTION99.01
4.1-38.040.25051520.20224463X-RAY DIFFRACTION99.53
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)
10.9086806917420.08512184462680.2920028742761.72862520002-0.2175496264222.88784197382-0.02235195690360.02143852761550.07419071717770.0849277935761-0.007023202038530.00451431519587-0.09282174439440.04811135284760.0174931791610.07905509650970.0004642212380850.004682359197460.1022971463870.009525451341920.0897213543583-27.3281950691-15.1070480182-15.0739324354
27.700269146990.29754394766-1.651906441943.87295258712-3.234936198429.30752630828-0.06833062818740.157103460481-0.52571799301-0.0134570847018-0.127988457047-1.700458872480.5608980778180.7082229537050.1775312314520.2232272403970.12547796395-0.008938772840630.3856481959390.01139449276370.37087768564312.3895394589-6.65420483883-12.7723031778
32.62055335836-0.6803547412480.07700477266852.876503315850.05182056515023.02486342781-0.00308570627418-0.0136879522299-0.00989081918840.0443017432478-0.00729050925341-0.2367241165960.07820993240370.2947352208440.00856579303020.1039665565490.0187528269923-0.01666241590730.1436116743270.001242063051270.148849986236-0.131121122672-0.57091387074-6.20794083602
43.542402806360.488156823280.6703354581731.315641866380.8186862395372.79139281245-0.1486621365760.0435295777768-0.003161830310940.06335581814540.05681431022240.1065323494670.18844312257-0.1198547799240.0852842799770.2382168123560.02047607468060.04469849316270.1149999120370.02430861441320.114924326185-32.481934299618.1595699713-7.78108440642
53.47308687734-0.1778478802091.710129001631.47907626595-0.05427802629122.644189478690.03547957624410.381841966980.119853450649-0.198612918246-0.100215486914-0.2248762691560.01976981040670.5062974823020.06694904798770.1597645020020.03377074407290.03178770042480.210930702810.03929459820520.153434935726-4.414774723762.05362669982-26.9674940669
60.843607870397-0.885373153447-0.3017191153733.286719548391.937247526823.75475447785-0.0800429832681-0.09809326885420.06836520073920.3157017404090.0790966637002-0.048006178247-0.1304905183350.1168901822730.0004014787611560.137932466732-0.023320905898-0.001813886073360.117501273620.008070924596360.107443834361-27.284850569828.1315727728-18.6784641832
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain KKC1 - 1211 - 123
22chain PPD2 - 121 - 11
33chain 'A' and (resid 1 through 127)AA1 - 1271 - 127
44chain 'A' and (resid 128 through 228)AA128 - 228128 - 228
55chain 'B' and (resid 1 through 106)BB1 - 1061 - 106
66chain 'B' and (resid 107 through 213)BB107 - 213107 - 215

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