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- PDB-7unz: Crystal structure of H2 nanobody in complex with PfCSS -

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Basic information

Entry
Database: PDB / ID: 7unz
TitleCrystal structure of H2 nanobody in complex with PfCSS
Components
  • Cysteine-rich small secreted protein CSS, putative
  • H2 Nanobody
KeywordsCELL INVASION / Plasmodium falciparum / 6-Cys protein / nanobody
Function / homologyMALONATE ION / Cysteine-rich small secreted protein CSS, putative
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsScally, S.W. / Cowman, A.F.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)637406 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1173049 Australia
CitationJournal: Nat Microbiol / Year: 2022
Title: PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum.
Authors: Scally, S.W. / Triglia, T. / Evelyn, C. / Seager, B.A. / Pasternak, M. / Lim, P.S. / Healer, J. / Geoghegan, N.D. / Adair, A. / Tham, W.H. / Dagley, L.F. / Rogers, K.L. / Cowman, A.F.
History
DepositionApr 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cysteine-rich small secreted protein CSS, putative
D: Cysteine-rich small secreted protein CSS, putative
C: H2 Nanobody
A: H2 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,55025
Polymers91,3984
Non-polymers4,15321
Water9,206511
1
B: Cysteine-rich small secreted protein CSS, putative
C: H2 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,82713
Polymers45,6992
Non-polymers2,12811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint34 kcal/mol
Surface area20320 Å2
MethodPISA
2
D: Cysteine-rich small secreted protein CSS, putative
A: H2 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,72412
Polymers45,6992
Non-polymers2,02510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint35 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.967, 190.428, 56.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 112)
d_2ens_1(chain "C" and resid 1 through 112)
d_1ens_2(chain "B" and (resid 27 through 142 or resid 144...
d_2ens_2(chain "D" and (resid 27 through 142 or resid 144...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNSERC1 - 119
d_21ens_1GLNSERD1 - 119
d_11ens_2LYSLEUA1 - 116
d_12ens_2GLYVALA118 - 120
d_13ens_2VALGLUA122 - 138
d_14ens_2ASPVALA140 - 141
d_15ens_2VALTYRA143 - 171
d_16ens_2VALLYSA173 - 212
d_17ens_2VALLYSA214 - 232
d_18ens_2PHEPHEA234
d_19ens_2LEUSERA236 - 243
d_110ens_2PHEALAA245 - 256
d_111ens_2ILELYSA258 - 264
d_112ens_2NAGNAGE
d_113ens_2NAGNAGF
d_114ens_2NAGNAGH
d_115ens_2NAGNAGI
d_116ens_2EDOEDOO
d_21ens_2LYSLEUP1 - 116
d_22ens_2GLYVALP118 - 120
d_23ens_2VALGLUP122 - 138
d_24ens_2ASPVALP140 - 141
d_25ens_2VALTYRP143 - 171
d_26ens_2VALLYSP173 - 212
d_27ens_2VALLYSP214 - 232
d_28ens_2PHEPHEP234
d_29ens_2LEUSERP236 - 243
d_210ens_2PHEALAP245 - 256
d_211ens_2ILELYSP258 - 264
d_212ens_2NAGNAGQ
d_213ens_2NAGNAGR
d_214ens_2NAGNAGT
d_215ens_2NAGNAGU
d_216ens_2EDOEDOD

NCS ensembles :
ID
ens_1
ens_2

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Components

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Protein / Antibody , 2 types, 4 molecules BDCA

#1: Protein Cysteine-rich small secreted protein CSS, putative


Mass: 32224.025 Da / Num. of mol.: 2 / Mutation: T263A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_1404700 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IM47
#2: Antibody H2 Nanobody


Mass: 13474.745 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 10 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 522 molecules

#6: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M bis-tris-propane pH 6.0, 17.5% (v/v) PEG3350, 0.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 2.03→48.99 Å / Num. obs: 83296 / % possible obs: 99.6 % / Redundancy: 13.5 % / Biso Wilson estimate: 34.98 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 14
Reflection shellResolution: 2.03→2.07 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4251 / CC1/2: 0.722 / Rpim(I) all: 0.444 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGV

5hgv


Resolution: 2.03→44.75 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.9679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2171 1914 2.43 %
Rwork0.1853 76912 -
obs0.186 78826 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.27 Å2
Refinement stepCycle: LAST / Resolution: 2.03→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6071 0 271 511 6853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256561
X-RAY DIFFRACTIONf_angle_d0.57638861
X-RAY DIFFRACTIONf_chiral_restr0.04861028
X-RAY DIFFRACTIONf_plane_restr0.00371126
X-RAY DIFFRACTIONf_dihedral_angle_d12.61082456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.475585514271
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS7.57038415417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.31171160.28934469X-RAY DIFFRACTION77.59
2.08-2.130.35081150.26344888X-RAY DIFFRACTION85.45
2.13-2.20.27131280.23835071X-RAY DIFFRACTION88.61
2.2-2.270.22311370.22385250X-RAY DIFFRACTION90.71
2.27-2.350.28441350.21935368X-RAY DIFFRACTION93.22
2.35-2.440.22561390.21145485X-RAY DIFFRACTION95.06
2.44-2.550.2541390.20285541X-RAY DIFFRACTION96.27
2.55-2.690.24881390.21585630X-RAY DIFFRACTION97.24
2.69-2.860.23721390.21675676X-RAY DIFFRACTION98.04
2.86-3.080.23591420.2015758X-RAY DIFFRACTION98.98
3.08-3.390.23231430.19795828X-RAY DIFFRACTION99.58
3.39-3.880.20221430.16675855X-RAY DIFFRACTION99.83
3.88-4.880.16381470.13865926X-RAY DIFFRACTION99.93
4.88-44.750.19811520.1696167X-RAY DIFFRACTION99.65
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)
15.777351561580.448603020169-3.30163239862.962182730461.446169652742.87704974139-0.2721319404711.112735852980.00162310543373-2.71767006925-0.1147394482930.7155080672271.62784285619-0.1272666814630.2949741007890.740707363322-0.06868405848690.03422669509330.54358270404-0.01591895305610.3913963070219.2930.36744.409
22.05676576973-0.204018476321.859618592390.987172431773-0.2705618840641.70235649359-0.004604023064050.00415748482569-0.319895297480.05914348117560.1192170162530.3270636458810.7798425863140.241698148736-0.1256560756420.638041520326-0.02029191038440.1433509762280.2707351521420.01732416888270.49275610127818.82824.4956.311
34.961721610190.8215929694573.561894883611.965626494132.204258173623.98591705554-0.2670178516060.1474550225240.653756348564-0.1239085526270.2728130433141.118248941580.186969871543-0.8574935174550.01827328414320.245636262027-0.03797565984690.02749484249980.4160699065480.1339135960660.5267475656978.97631.86357.446
44.621827290161.055969456320.5187911050258.04680470635-1.521105647334.65200790882-0.113121387408-0.44255299189-0.3025586391060.269142205377-0.031797629044-0.2270857188640.434228703530.3537315227180.1435638972620.3158390735620.01981019235030.03761436241990.2873228034480.08792913697740.27391143543720.85529.68762.604
53.146504324471.59694321874-0.8999834011046.39055330763-1.718295852744.59260768884-0.1785114312-0.0213916481595-0.229917793533-0.2195634270.2542922722730.5177163479430.591081160877-0.39714347307-0.01000419018150.242157911716-0.05214695211650.02788139540380.3401160859170.05264909351480.36507853302312.47229.64356.406
62.4471377132-1.18468020911.311829580573.93794252875-1.189426734041.96898163929-0.0259887834335-0.520277038036-0.3717382999720.3308754397520.5503718751421.030334419510.0911863782585-0.437319269956-0.38532341080.3341030231310.04586062603380.02801195386230.5030743543380.2132359732520.60473357258614.568126.58812.36
72.96545220623-0.4161936823541.187889097513.75575054793-0.3215919236022.215726194560.0323908758794-0.00478489126540.159503523947-0.1119248746690.09220857229120.204781478653-0.0818395093355-0.0845255487308-0.103331607170.2322713805860.00101300783830.04722331545760.2111244677230.02231368111280.19111619222138.638103.85127.736
82.812993971241.45413832223-0.9367096981195.12860461517-1.164443059252.18287962647-0.07624478266010.5058989609790.331212109554-0.3652306683910.3833401538760.706715649948-0.104497951732-0.314209933088-0.2377618673880.280178473395-0.0482560011922-0.01193106980450.4258496102660.1002416456290.41275217019612.79254.31243.999
93.069732736820.757842588753-1.369004118083.56284919358-0.3607522703152.322414074350.06051023470550.0858552575461-0.134421534268-0.009426674991690.04772161139620.1361599800590.0978591274552-0.112315625522-0.09229172776230.24729495612-0.0326104370759-0.04681979089150.2087535272570.005086665874810.20618358299437.34476.21929.297
108.18772136793-2.86557845772.749687849727.01360305181-0.4233760873936.60536308312-0.313835885598-0.3868805510510.3768844605640.7221527585610.5608557354980.500199480355-0.973391880772-0.429107775734-0.1874486717040.255268524638-0.011341936552-0.003201178813140.2803080543390.05195791172630.35893282637816.368158.6710.49
116.96519016137-2.53822146157-0.1155573299828.09180631471.455780928542.61680803062-0.0696876532263-0.3437672196790.1324092292350.6658947265560.0991102619602-0.554907916895-0.1189146957370.67042654208-0.03887787335380.305930554682-0.0594412756174-0.07015791934240.4291418714130.03927865798740.29000869907226.29150.9872.612
122.151519747621.10546228504-1.159128838361.814720833851.558754429484.353884616160.0429437569442-0.280615356624-0.5453314859030.2539106922490.08638489117361.06774164463-0.0704655962682-0.716320224876-0.08052567103380.238471105250.0135287382005-0.01940564940940.4153414762980.1503176162620.53698439756311.085148.643-1.599
136.835859855791.82257899385-5.293002866472.07889810443-0.02342331001695.48343492573-0.03150657258130.6703335991850.238950220169-0.4620977206610.08838907235430.00401179032040.171211689680.153513415518-0.07662084704120.262852187421-0.0102803885096-0.03417760101610.3520172277770.08055491107260.29695724687322.602145.582-7.402
148.0052801856-0.8646215785551.98960277086.49828416929-1.453979760086.41763912189-0.08250901479930.5976380637960.350035428317-0.088654947951-0.0217079186164-0.060026844559-0.4119079910630.3254280036350.1355374433460.275503980839-0.0457562060478-0.03586477405190.3302481428830.09754607728090.2201236426123.093153.167-6.551
153.18651208264-2.219050718491.288321108415.58191660694-1.438194207364.5585963424-0.1466961335680.1300789941130.03862271575080.1818587869830.2653331085270.635138158211-0.492449240375-0.282340257646-0.06939550425280.190198233826-0.00382657134836-0.02919148114310.3669999083390.1290740625620.41451702120913.972151.758-0.987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:5 )A1 - 5
2X-RAY DIFFRACTION2( CHAIN A AND RESID 6:33 )A6 - 33
3X-RAY DIFFRACTION3( CHAIN A AND RESID 34:45 )A34 - 45
4X-RAY DIFFRACTION4( CHAIN A AND RESID 46:82 )A46 - 82
5X-RAY DIFFRACTION5( CHAIN A AND RESID 83:112 )A83 - 112
6X-RAY DIFFRACTION6( CHAIN B AND RESID 27:150 )B27 - 150
7X-RAY DIFFRACTION7( CHAIN B AND RESID 151:292 )B151 - 292
8X-RAY DIFFRACTION8( CHAIN D AND RESID 27:150 )D27 - 150
9X-RAY DIFFRACTION9( CHAIN D AND RESID 151:290 )D151 - 290
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:17 )C1 - 17
11X-RAY DIFFRACTION11( CHAIN C AND RESID 18:33 )C18 - 33
12X-RAY DIFFRACTION12( CHAIN C AND RESID 34:45 )C34 - 45
13X-RAY DIFFRACTION13( CHAIN C AND RESID 46:59 )C46 - 59
14X-RAY DIFFRACTION14( CHAIN C AND RESID 60:82 )C60 - 82
15X-RAY DIFFRACTION15( CHAIN C AND RESID 83:114 )C83 - 114

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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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