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- PDB-2yad: BRICHOS domain of Surfactant protein C precursor protein -

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Basic information

Entry
Database: PDB / ID: 2yad
TitleBRICHOS domain of Surfactant protein C precursor protein
ComponentsSURFACTANT PROTEIN C BRICHOS DOMAIN
KeywordsSURFACTANT PROTEIN / PULMONARY SURFACTANT SYSTEM / INTERSTITIAL LUNG DISEASE / AMYLOID / CHAPERONE
Function / homology
Function and homology information


Defective pro-SFTPC causes SMDP2 and RDS / multivesicular body lumen / lamellar body / protein metabolic process => GO:0019538 / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism ...Defective pro-SFTPC causes SMDP2 and RDS / multivesicular body lumen / lamellar body / protein metabolic process => GO:0019538 / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Surfactant metabolism / endoplasmic reticulum membrane / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Enolase-like; domain 1 - #150 / Pulmonary surfactant-associated protein C / Pulmonary surfactant proteins / BRICHOS / Surfactant protein C, N-terminal propeptide / Surfactant-associated polypeptide, palmitoylation site / Surfactant protein C, N terminal propeptide / Surfactant associated polypeptide SP-C palmitoylation sites. / BRICHOS domain / BRICHOS domain ...Enolase-like; domain 1 - #150 / Pulmonary surfactant-associated protein C / Pulmonary surfactant proteins / BRICHOS / Surfactant protein C, N-terminal propeptide / Surfactant-associated polypeptide, palmitoylation site / Surfactant protein C, N terminal propeptide / Surfactant associated polypeptide SP-C palmitoylation sites. / BRICHOS domain / BRICHOS domain / BRICHOS domain profile. / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pulmonary surfactant-associated protein C / Pulmonary surfactant-associated protein C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsAskarieh, G. / Siponen, M.I. / Willander, H. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. ...Askarieh, G. / Siponen, M.I. / Willander, H. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / Jornvall, H. / Presto, J. / Johansson, J. / Arrowsmith, C.H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Nordlund, P. / Persson, C. / Schuler, H. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Berglund, H. / Knight, S.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: High Resolution Structure of a Bricos Domain and its Implications for Anti-Amyloid Chaperone Activity on Lung Surgactant Protein C.
Authors: Willander, H. / Askarieh, G. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / ...Authors: Willander, H. / Askarieh, G. / Landreh, M. / Westermark, P. / Nordling, K. / Keranen, H. / Hermansson, E. / Hamvas, A. / Nogee, L.M. / Bergman, T. / Saenz, A. / Casals, C. / Aqvist, J. / Jornvall, H. / Berglund, H. / Presto, J. / Knight, S.D. / Johansson, J.
History
DepositionFeb 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2Aug 13, 2014Group: Refinement description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SURFACTANT PROTEIN C BRICHOS DOMAIN
B: SURFACTANT PROTEIN C BRICHOS DOMAIN
C: SURFACTANT PROTEIN C BRICHOS DOMAIN
D: SURFACTANT PROTEIN C BRICHOS DOMAIN
E: SURFACTANT PROTEIN C BRICHOS DOMAIN
F: SURFACTANT PROTEIN C BRICHOS DOMAIN


Theoretical massNumber of molelcules
Total (without water)112,2536
Polymers112,2536
Non-polymers00
Water1,874104
1
A: SURFACTANT PROTEIN C BRICHOS DOMAIN
B: SURFACTANT PROTEIN C BRICHOS DOMAIN
E: SURFACTANT PROTEIN C BRICHOS DOMAIN


Theoretical massNumber of molelcules
Total (without water)56,1273
Polymers56,1273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-19.6 kcal/mol
Surface area10770 Å2
MethodPISA
2
C: SURFACTANT PROTEIN C BRICHOS DOMAIN
D: SURFACTANT PROTEIN C BRICHOS DOMAIN
F: SURFACTANT PROTEIN C BRICHOS DOMAIN


Theoretical massNumber of molelcules
Total (without water)56,1273
Polymers56,1273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-21.5 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.046, 39.329, 114.756
Angle α, β, γ (deg.)90.00, 99.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SURFACTANT PROTEIN C BRICHOS DOMAIN /


Mass: 18708.883 Da / Num. of mol.: 6 / Fragment: RESIDUES 15-144
Source method: isolated from a genetically manipulated source
Details: EXPRESSED N-TERMINAL SEQUENCE DIFFERS FROM UNIPROT REFERENCE
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI B(DE3) / Variant (production host): PLYSS / References: UniProt: E5RI64, UniProt: P11686*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPRESSED PROTEIN DIFFERS FROM THE UNIPROT REFERENCE SEQUENCE AT THE N-TERMINUS. THE SEQUENCE ...THE EXPRESSED PROTEIN DIFFERS FROM THE UNIPROT REFERENCE SEQUENCE AT THE N-TERMINUS. THE SEQUENCE HMSQKHTEM IS PART OF PROTEIN AND NOT THE EXPRESSION TAG. DATABASE REFERENCE FOR THE EXPRESSED PROTEIN IS NCBI REFERENCE NP_003009.2. WITH TRUNCATION OF FIRST 58 RESIDUES AND S-TAG REMOVED BY IN SITU PROTEOLYSIS DURING CRYSTALLIZATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.32 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97925
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 34299 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 37.52 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.1

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.2→27.43 Å / Cor.coef. Fo:Fc: 0.9366 / Cor.coef. Fo:Fc free: 0.9078 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IN SITU PROTEOLYSIS. UNSTRUCTURED LOOP BETWEEN HELIX 1 AND HELIX 2 AS WELL AS THE N-TERMINAL S-TAG AND LINKER ARE FULLY OR PARTLY CLEAVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1476 5.09 %RANDOM
Rwork0.1902 ---
obs0.1918 29015 --
Displacement parametersBiso mean: 46.33 Å2
Baniso -1Baniso -2Baniso -3
1-6.7617 Å20 Å22.4415 Å2
2---11.1612 Å20 Å2
3---4.3994 Å2
Refine analyzeLuzzati coordinate error obs: 0.324 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 104 3599
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013687HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075050HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1616SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes544HARMONIC5
X-RAY DIFFRACTIONt_it3687HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion2.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion523SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4285SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.183 96 4.43 %
Rwork0.1968 2070 -
all0.1962 2166 -
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)
17.7502-1.45321.43220.14430.3147.2124-0.1863-0.91490.65730.1159-0.0078-0.1043-0.4228-0.31170.194-0.07560.0416-0.06360.1052-0.0932-0.149146.994910.993844.1835
24.8662-0.74041.238900.76085.07080.0340.28540.0867-0.1972-0.1045-0.03-0.2180.58240.0705-0.09750.02270.00490.08310.0163-0.095451.80075.184324.0876
32.9928-1.17150.5881.22510.37044.0375-0.0399-0.02160.0269-0.00740.0489-0.0090.0361-0.0207-0.0090.0066-0.02940.0086-0.07570.0053-0.054629.99796.02768.7869
45.251-1.46140.69470.24610.9034.7957-0.0923-0.82030.290.0579-0.01240.0606-0.5426-0.45270.1047-0.07780.1347-0.03590.1009-0.1093-0.096825.394214.232128.0482
57.0077-0.08851.37810.77671.96188.6358-0.07020.16280.3241-0.1347-0.0309-0.193-0.32381.13160.1012-0.1783-0.0050.01470.2687-0.0092-0.197967.35476.610939.1877
65.2674-1.1904-0.06831.60931.91735.8157-0.1169-0.16190.3212-0.23-0.17490.1841-0.5322-0.7930.2918-0.10930.1759-0.03270.1348-0.0941-0.108410.449415.406312.665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A90 - A149 OR A181 - A197)
2X-RAY DIFFRACTION2(B89 - B149 OR B180 - B197)
3X-RAY DIFFRACTION3(C87 - C151 OR C180 - C197)
4X-RAY DIFFRACTION4(D88 - D148 OR D180 - D197)
5X-RAY DIFFRACTION5(E89 - E149 OR E180 - E197)
6X-RAY DIFFRACTION6(F89 - F148 OR F181 - F197)

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