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- PDB-4au2: Crystal Structure of a Hsp47-collagen complex -

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Basic information

Entry
Database: PDB / ID: 4au2
TitleCrystal Structure of a Hsp47-collagen complex
Components
  • 15ER COLLAGEN MODEL PEPTIDE 15-R8
  • SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)Serpin
KeywordsCHAPERONE/PEPTIDE / CHAPERONE-PEPTIDE COMPLEX / CHAPERONE / HEAT SHOCK PROTEIN
Function / homology
Function and homology information


Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / collagen trimer / positive regulation of cell-substrate adhesion / Collagen degradation / collagen binding / serine-type endopeptidase inhibitor activity / collagen-containing extracellular matrix / endoplasmic reticulum lumen / Golgi apparatus ...Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / collagen trimer / positive regulation of cell-substrate adhesion / Collagen degradation / collagen binding / serine-type endopeptidase inhibitor activity / collagen-containing extracellular matrix / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
EMI domain / Serpin H1, serpin domain / EMI domain / EMI domain profile. / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. ...EMI domain / Serpin H1, serpin domain / EMI domain / EMI domain profile. / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serpin H1 / Collagen alpha-1(XXVI) chain
Similarity search - Component
Biological speciesCANIS LUPUS FAMILIARIS (dog)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWidmer, C. / Gebauer, J.M. / Brunstein, E. / Drogemuller, C. / Leeb, T. / Baumann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular Basis for the Action of the Collagen-Specific Chaperone Hsp47/Serpinh1 and its Structure-Specific Client Recognition.
Authors: Widmer, C. / Gebauer, J.M. / Brunstein, E. / Rosenbaum, S. / Zaucke, F. / Drogemuller, C. / Leeb, T. / Baumann, U.
History
DepositionMay 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Apr 1, 2015Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
B: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
C: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
D: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
E: 15ER COLLAGEN MODEL PEPTIDE 15-R8
F: 15ER COLLAGEN MODEL PEPTIDE 15-R8
G: 15ER COLLAGEN MODEL PEPTIDE 15-R8
H: 15ER COLLAGEN MODEL PEPTIDE 15-R8
I: 15ER COLLAGEN MODEL PEPTIDE 15-R8
J: 15ER COLLAGEN MODEL PEPTIDE 15-R8


Theoretical massNumber of molelcules
Total (without water)184,94410
Polymers184,94410
Non-polymers00
Water4,216234
1
A: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
B: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
E: 15ER COLLAGEN MODEL PEPTIDE 15-R8
F: 15ER COLLAGEN MODEL PEPTIDE 15-R8
G: 15ER COLLAGEN MODEL PEPTIDE 15-R8


Theoretical massNumber of molelcules
Total (without water)92,4725
Polymers92,4725
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-38.1 kcal/mol
Surface area32340 Å2
MethodPISA
2
C: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
D: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
H: 15ER COLLAGEN MODEL PEPTIDE 15-R8
I: 15ER COLLAGEN MODEL PEPTIDE 15-R8
J: 15ER COLLAGEN MODEL PEPTIDE 15-R8


Theoretical massNumber of molelcules
Total (without water)92,4725
Polymers92,4725
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-39.6 kcal/mol
Surface area31480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.498, 92.784, 100.458
Angle α, β, γ (deg.)95.24, 98.95, 96.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1) / Serpin / HSP47


Mass: 44283.680 Da / Num. of mol.: 4 / Fragment: RESIDUES 35-418
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HISTAG, FIRST 35 RESIDUES MISSING / Source: (gene. exp.) CANIS LUPUS FAMILIARIS (dog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7C419
#2: Protein/peptide
15ER COLLAGEN MODEL PEPTIDE 15-R8


Mass: 1301.495 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: N-TERMINAL ACETYL GROUP, C-TERMINAL AMIDE / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q96A83*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.25 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→70.5 Å / Num. obs: 70114 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 56.54 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.2
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.3 / % possible all: 9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→98.62 Å / Cor.coef. Fo:Fc: 0.9447 / Cor.coef. Fo:Fc free: 0.9275 / SU R Cruickshank DPI: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.23
Details: SOME DISORDERED SIDECHAINS CUT TO ALA REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 3535 5.04 %RANDOM
Rwork0.2025 ---
obs0.2044 70107 96.4 %-
Displacement parametersBiso mean: 74.15 Å2
Baniso -1Baniso -2Baniso -3
1--8.993 Å20.056 Å29.3588 Å2
2--6.4162 Å2-2.2349 Å2
3---2.5769 Å2
Refine analyzeLuzzati coordinate error obs: 0.415 Å
Refinement stepCycle: LAST / Resolution: 2.3→98.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11663 0 0 234 11897
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911927HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1316107HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4118SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes247HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1716HARMONIC5
X-RAY DIFFRACTIONt_it11927HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion19.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1502SEMIHARMONIC5
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_contact12964SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2758 246 4.92 %
Rwork0.2449 4752 -
all0.2464 4998 -
obs--96.4 %
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)
11.51820.35120.62533.07090.85972.2027-0.1342-0.13810.12770.1117-0.05940.0129-0.1407-0.0430.1936-0.3011-0.03160.022-0.08060.0421-0.067431.2158-123.825322.2295
22.1462-0.07781.86262.80350.65973.7798-0.0237-0.2309-0.03160.74930.1754-0.70870.13480.1464-0.1516-0.05310.0403-0.2272-0.2931-0.0401-0.170751.7047-84.964567.5712
32.09410.20741.76663.55072.24884.6786-0.3707-0.12560.3592-0.4851-0.14730.3256-0.938-0.4450.5180.00010.0524-0.2096-0.31060.0194-0.231231.8823-29.606189.8066
40.8634-0.0614-1.041.0889-0.44164.00210.0985-0.00370.1114-0.04830.0679-0.2698-0.05860.0708-0.1664-0.0697-0.0668-0.0535-0.22720.0234-0.069340.3064-61.528236.9087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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