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- PDB-4k12: Structural Basis for Host Specificity of Factor H Binding by Stre... -

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Basic information

Entry
Database: PDB / ID: 4k12
TitleStructural Basis for Host Specificity of Factor H Binding by Streptococcus pneumoniae
Components
  • Choline binding protein A
  • Complement factor HFactor H
KeywordsIMMUNE SYSTEM/CHOLINE BINDING PROTEIN / protein-protein complex / Complement-binding complex / IMMUNE SYSTEM-CHOLINE BINDING PROTEIN complex
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Receptor-associated Protein - #20 / Receptor-associated Protein / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon ...Receptor-associated Protein - #20 / Receptor-associated Protein / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Complement factor H
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.079 Å
AuthorsLiu, A. / Achila, D. / Banerjee, R. / Martinez-Hackert, E. / Li, Y. / Yan, H.
CitationJournal: Biochem.J. / Year: 2015
Title: Structural determinants of host specificity of complement Factor H recruitment by Streptococcus pneumoniae.
Authors: Achila, D. / Liu, A. / Banerjee, R. / Li, Y. / Martinez-Hackert, E. / Zhang, J.R. / Yan, H.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement factor H
B: Choline binding protein A


Theoretical massNumber of molelcules
Total (without water)17,0082
Polymers17,0082
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-6 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.587, 48.985, 71.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Complement factor H / Factor H / Factor H protein / H factor 1


Mass: 7270.953 Da / Num. of mol.: 1 / Fragment: sushi domain (UNP residues 508-567)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P08603
#2: Protein Choline binding protein A / CbpA


Mass: 9737.062 Da / Num. of mol.: 1 / Fragment: UNP residues 68-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SPAR136_2333 / Production host: Escherichia coli (E. coli) / References: UniProt: G6W2B2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1442.45
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop4.620% PEG3500, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop4.620% PEG3500, 0.1 M sodium acetate, soaked in 0.5 M sodium iodide, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97856
SYNCHROTRONAPS 21-ID-D21.45868
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDOct 14, 2012
MARMOSAIC 300 mm CCD2CCDOct 14, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond(111)SINGLE WAVELENGTHMx-ray1
2KOHZU Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
21.458681
ReflectionRedundancy: 13.5 % / Av σ(I) over netI: 35.17 / Number: 93440 / Rmerge(I) obs: 0.097 / Χ2: 1.05 / D res high: 2.29 Å / D res low: 50 Å / Num. obs: 6909 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.215099.510.080.67912.2
4.936.2110010.0810.76213.2
4.314.9310010.0830.88413.2
3.924.3199.710.0891.06513.1
3.633.9299.710.0880.9913.2
3.423.6310010.0921.08913.6
3.253.4299.710.0971.06913.7
3.113.2510010.1021.11713.6
2.993.1110010.1121.19413.8
2.892.9910010.1251.13813.9
2.792.8910010.1241.11913.9
2.722.7910010.1361.13813.9
2.642.7210010.1521.16214
2.582.6410010.1561.07314
2.522.5810010.1631.08813.9
2.472.5210010.1821.09614.1
2.422.4710010.1911.10313.7
2.372.4210010.2051.15914
2.332.3710010.2071.13213.7
2.292.3376.210.2211.06811.8
ReflectionResolution: 1.079→50 Å / Num. all: 63403 / Num. obs: 63150 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.044 / Χ2: 1.039 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.079-1.125.90.35962520.9141,299.7
1.12-1.166.90.25262301.0051,2100
1.16-1.2270.19462571.0711,2100
1.22-1.2870.15262801.1121,2100
1.28-1.367.10.12662901.1471,2100
1.36-1.477.20.09162791.0761,2100
1.47-1.617.20.06563271.0421,2100
1.61-1.857.10.05563561.0681,2100
1.85-2.337.20.03764090.9641,2100
2.33-506.80.0364700.9721,296.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å40.39 Å
Translation2.5 Å40.39 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.079→19.964 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.9283 / SU ML: 0.24 / σ(F): 1.37 / Phase error: 12.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 3201 5.08 %RANDOM
Rwork0.1544 ---
obs0.1552 63060 99.53 %-
all-63403 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.282 Å2 / ksol: 0.421 e/Å3
Displacement parametersBiso max: 43.73 Å2 / Biso mean: 14.7118 Å2 / Biso min: 6.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.9173 Å2-0 Å20 Å2
2---1.5749 Å2-0 Å2
3---2.4922 Å2
Refinement stepCycle: LAST / Resolution: 1.079→19.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 0 255 1405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111268
X-RAY DIFFRACTIONf_angle_d1.2431733
X-RAY DIFFRACTIONf_chiral_restr0.088195
X-RAY DIFFRACTIONf_plane_restr0.006224
X-RAY DIFFRACTIONf_dihedral_angle_d9.305505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.079-1.09560.30751250.27432541266697
1.0956-1.11270.28111490.230325472696100
1.1127-1.1310.18521410.180425752716100
1.131-1.15040.16521230.166425982721100
1.1504-1.17140.17341310.142625722703100
1.1714-1.19390.15741490.135525722721100
1.1939-1.21830.17141380.132925842722100
1.2183-1.24470.12661390.125525632702100
1.2447-1.27370.15131450.127725942739100
1.2737-1.30550.16341280.127626182746100
1.3055-1.34080.12281440.121925802724100
1.3408-1.38030.12831510.122725972748100
1.3803-1.42480.14771540.12425672721100
1.4248-1.47570.14211600.114725812741100
1.4757-1.53480.12391210.114326402761100
1.5348-1.60460.13071580.117725972755100
1.6046-1.68920.14671460.12426252771100
1.6892-1.79490.14641400.134825982738100
1.7949-1.93340.15371150.145126652780100
1.9334-2.12780.16931250.146826552780100
2.1278-2.43520.16351370.155726642801100
2.4352-3.06630.19561510.171726902841100
3.0663-19.96710.20981310.19562636276794

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