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- PDB-4au4: Crystal Structure of Hsp47 -

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Basic information

Entry
Database: PDB / ID: 4au4
TitleCrystal Structure of Hsp47
ComponentsSERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
KeywordsCHAPERONE
Function / homology
Function and homology information


collagen trimer / collagen fibril organization / collagen binding / serine-type endopeptidase inhibitor activity / endoplasmic reticulum / extracellular space
Similarity search - Function
Serpin H1, serpin domain / 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. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Serpin H1, serpin domain / 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. / 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
Biological speciesCANIS LUPUS FAMILIARIS (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsWidmer, C. / Gebauer, J.M. / Brunstein, E. / Rodenbaum, S. / Zaucke, F. / 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 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
F: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
G: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)309,9867
Polymers309,9867
Non-polymers00
Water00
1
A: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)


Theoretical massNumber of molelcules
Total (without water)44,2841
Polymers44,2841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)178.780, 115.110, 188.275
Angle α, β, γ (deg.)90.00, 107.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44283.680 Da / Num. of mol.: 7
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

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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: 3.04 Å3/Da / Density % sol: 59.56 % / 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: MARRESEARCH / Detector: CCD / Date: Jul 3, 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: 2.97→50 Å / Num. obs: 73293 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 62.12 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.02
Reflection shellResolution: 2.97→3.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.07 / % possible all: 95.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→48.17 Å / Cor.coef. Fo:Fc: 0.9157 / Cor.coef. Fo:Fc free: 0.8834 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.331
Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 3660 4.99 %RANDOM
Rwork0.1805 ---
obs0.1825 73293 97.45 %-
Displacement parametersBiso mean: 52.02 Å2
Baniso -1Baniso -2Baniso -3
1-3.4851 Å20 Å29.7595 Å2
2---7.7787 Å20 Å2
3---4.2935 Å2
Refine analyzeLuzzati coordinate error obs: 0.381 Å
Refinement stepCycle: LAST / Resolution: 2.97→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20207 0 0 0 20207
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0120612HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.227782HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7326SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes453HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2964HARMONIC5
X-RAY DIFFRACTIONt_it20612HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion21.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2621SEMIHARMONIC5
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_contact22298SEMIHARMONIC4
LS refinement shellResolution: 2.97→3.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3255 254 4.85 %
Rwork0.2528 4978 -
all0.2563 5232 -
obs--97.45 %
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)
11.8007-1.0764-0.08111.00290.16830.4578-0.0483-0.08750.07720.07910.0154-0.0242-0.0347-0.12230.0329-0.0320.02940.0062-0.0532-0.0124-0.0695-55.752940.5239240.7978
21.86811.7362-0.58021.853-0.7220.36680.0755-0.196-0.15310.1626-0.1063-0.1009-0.06660.0210.03090.0412-0.0085-0.0544-0.06810.02380.0281-14.679665.0115223.6812
30.9463-0.14080.10691.5-1.2053.0771-0.0065-0.2098-0.03350.15230.05490.08350.1061-0.2099-0.04840.0157-0.0081-0.0102-0.01180.0191-0.0464-72.840964.3892190.9324
42.4694-0.37520.59450.9869-0.57991.60060.2492-0.1488-0.5829-0.0993-0.07570.07910.46850.0917-0.17350.17180.0543-0.0544-0.0620.03860.1252-24.9395110.877250.0893
51.62051.02440.6612.68490.69411.5879-0.105-0.00270.38320.0516-0.01740.1212-0.30090.03030.12240.06620.031-0.0485-0.0813-0.02850.0185-23.903599.0546205.7211
61.3335-0.50490.49741.5352-0.14061.52530.21280.47850.3774-0.3372-0.1565-0.0809-0.12970.2443-0.05630.05590.07880.10570.11810.1391-0.0039-86.459980.4605241.5138
73.3112-0.73780.74891.19890.26782.41630.08460.69950.0779-0.1641-0.0103-0.21830.2110.6236-0.07440.0780.0521-0.0070.1417-0.0028-0.0195-54.828222.8905204.661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G

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