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- PDB-4au3: Crystal Structure of a Hsp47-collagen complex -

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Basic information

Entry
Database: PDB / ID: 4au3
TitleCrystal Structure of a Hsp47-collagen complex
Components
  • 18ER COLLAGEN MODEL PEPTIDE 15-R8
  • SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47 ), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
  • SERPYIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47 ), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
KeywordsCHAPERONE/PEPTIDE / CHAPERONE-PEPTIDE COMPLEX / CHAPERONE
Function / homology
Function and homology information


Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / negative regulation of endopeptidase activity / collagen trimer / collagen fibril organization / positive regulation of cell-substrate adhesion / Collagen degradation / collagen binding / serine-type endopeptidase inhibitor activity ...Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / negative regulation of endopeptidase activity / collagen trimer / collagen fibril organization / 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
Serpin H1 / 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 ...Serpin H1 / 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
Collagen-binding protein / Collagen alpha-1(XXVI) chain
Similarity search - Component
Biological speciesCANIS LUPUS FAMILIARIS (dog)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å
Model type detailsCA ATOMS ONLY, CHAIN B
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

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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: SERPYIN 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: 18ER COLLAGEN MODEL PEPTIDE 15-R8
F: 18ER COLLAGEN MODEL PEPTIDE 15-R8
G: 18ER COLLAGEN MODEL PEPTIDE 15-R8
H: 18ER COLLAGEN MODEL PEPTIDE 15-R8
I: 18ER COLLAGEN MODEL PEPTIDE 15-R8
J: 18ER COLLAGEN MODEL PEPTIDE 15-R8


Theoretical massNumber of molelcules
Total (without water)189,24810
Polymers189,24810
Non-polymers00
Water00
1
A: SERPIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47 ), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
B: SERPYIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47 ), MEMBER 1, (COLLAGEN BINDING PROTEIN 1)
E: 18ER COLLAGEN MODEL PEPTIDE 15-R8
F: 18ER COLLAGEN MODEL PEPTIDE 15-R8
G: 18ER COLLAGEN MODEL PEPTIDE 15-R8


Theoretical massNumber of molelcules
Total (without water)94,6325
Polymers94,6325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-39.2 kcal/mol
Surface area32480 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: 18ER COLLAGEN MODEL PEPTIDE 15-R8
I: 18ER COLLAGEN MODEL PEPTIDE 15-R8
J: 18ER COLLAGEN MODEL PEPTIDE 15-R8


Theoretical massNumber of molelcules
Total (without water)94,6165
Polymers94,6165
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-40 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.260, 101.260, 366.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 44893.309 Da / Num. of mol.: 3 / Fragment: RESIDUES 35-418
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HISTAG / Source: (gene. exp.) CANIS LUPUS FAMILIARIS (dog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E2RHY7
#2: Protein SERPYIN PEPTIDASE INHIBITOR, CLADE H (HEAT SHOCK PROTEIN 47 ), MEMBER 1, (COLLAGEN BINDING PROTEIN 1) / HSP47


Mass: 44909.309 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-418
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HISTAG / Source: (gene. exp.) CANIS LUPUS FAMILIARIS (dog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E2RHY7
#3: Protein/peptide
18ER COLLAGEN MODEL PEPTIDE 15-R8


Mass: 1609.828 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
Sequence detailsCHEMICALLY SYNTHESIZED N-TERMINUS ACETYLATED, C-TERMINUS AMIDATED

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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: 2.57 Å3/Da / Density % sol: 52.14 % / 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: 0.9794
DetectorType: MARMOSAIC 225 mm CCD / 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: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 48652 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 76.89 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.4
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 1.6 / % possible all: 94.7

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Processing

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

Resolution: 2.78→91.74 Å / Cor.coef. Fo:Fc: 0.9314 / Cor.coef. Fo:Fc free: 0.9021 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.998 / SU Rfree Blow DPI: 0.318
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 2459 5.05 %RANDOM
Rwork0.2029 ---
obs0.2044 48652 98.69 %-
Displacement parametersBiso mean: 77.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.8688 Å20 Å20 Å2
2---1.8688 Å20 Å2
3---3.7375 Å2
Refine analyzeLuzzati coordinate error obs: 0.474 Å
Refinement stepCycle: LAST / Resolution: 2.78→91.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12171 0 0 0 12171
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112455HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.216825HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4324SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1793HARMONIC5
X-RAY DIFFRACTIONt_it12455HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion20.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1565SEMIHARMONIC5
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_contact13613SEMIHARMONIC4
LS refinement shellResolution: 2.78→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4108 170 5.38 %
Rwork0.3004 2988 -
all0.3064 3158 -
obs--98.69 %
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)
12.3038-0.6597-1.0581.8380.24582.5064-0.1263-0.1055-0.17410.1165-0.0307-0.00040.1329-0.32040.157-0.0387-0.04670.032-0.079-0.0517-0.0456-48.0623133.054217.862
23.3143-1.2318-0.78511.75350.27371.2444-0.1130.1097-0.3141-0.0566-0.02490.04490.2522-0.21860.1379-0.0445-0.05470.0745-0.2134-0.0649-0.0855-37.6535121.057208.952
36.3564-1.8999-1.57873.74042.00872.8555-0.0322-0.2865-0.13590.12650.1626-0.38420.1962-0.13-0.13040.0664-0.01820.1514-0.1752-0.01760.0877-31.0348116.512207.639
43.1317-0.2787-1.27860-1.09197.03950.26260.76010.3091-1.0844-0.35450.06070.5019-0.16260.09180.41730.1507-0.0224-0.3333-0.0074-0.2899-12.101395.4602152.584
55.28982.4651-1.66530.13680.1778.3429-0.06590.64380.3294-0.0848-0.0272-0.15590.70480.37290.09310.4750.27950.304-0.17380.0351-0.3432.772990.9345154.011
61.9568-5.1566-4.095110.75793.11184.32180.09530.0575-0.0233-0.4999-0.1552-0.33110.63850.08790.05990.30760.24580.1494-0.2088-0.0386-0.13011.639280.5647165.475
71.114-1.03830.29724.72920.48794.02340.20820.0981-0.0083-1.014-0.16610.56270.1665-0.4032-0.0421-0.0629-0.0081-0.0078-0.2811-0.0484-0.1679-16.796598.5577170.968
81.2252-0.15711.02124.7920.32813.90550.15690.15570.1712-0.9586-0.01480.20950.33140.201-0.14210.0890.01230.0701-0.176-0.0525-0.1701-12.42796.1256170.304
94.00980.8463.77593.46410.24069.45020.29580.4668-0.972-0.5426-0.00451.08210.3003-0.2251-0.2913-0.42970.1961-0.2655-0.2299-0.3040.4011-2.172544.8077149.836
105.01-0.77670.32222.7804-0.10625.4857-0.0286-0.0831-1.0725-0.0053-0.05261.08850.1793-0.76150.0812-0.4131-0.04560.0129-0.5355-0.11370.6079-0.120328.9249160.082
114.6691-2.0750.04764.58490.03821.373-0.00870.1354-0.6198-0.0505-0.06511.0885-0.359-0.27970.0738-0.17860.0924-0.0194-0.3136-0.0439-0.129510.86849.8001161.488
128.0552-0.66160.41244.17020.97930.84280.00950.1468-0.321-0.0891-0.06120.269-0.2663-0.22110.05170.02290.0444-0.0357-0.20830.0001-0.115818.662152.6559162.544
131.8806-1.12130.97982.73040.77652.6908-0.4963-0.40070.60160.68240.1844-0.5033-0.96380.30180.31180.3260.159-0.304-0.2661-0.186-0.293750.667171.9538213.637
141.626-0.36641.17861.66940.16083.8707-0.608-0.21260.46620.43030.2452-0.1648-1.0317-0.16630.36280.27290.2181-0.2385-0.3179-0.0938-0.263838.981669.4748200.211
153.2424-1.41071.528500.03164.5398-0.3537-0.08220.16250.13340.0448-0.114-0.5477-0.00620.30890.17340.0893-0.133-0.1989-0.0503-0.176435.618164.3027194.133
161.9614-4.9382-1.69584.4951-0.45963.4943-0.06660.06320.09380.3367-0.2313-0.05160.2564-0.12960.2979-0.03730.06510.1812-0.1522-0.1833-0.0923-19.7079105.885195.717
170.0374-3.8024-2.04482.41561.72120.6326-0.0659-0.15710.1780.21910.3615-0.1246-0.04040.1024-0.2956-0.1161-0.07210.2297-0.3398-0.0966-0.0664-18.6072109.678195.603
185.8817-4.0816-0.84461.4367-1.5482.31420.0622-0.07490.151-0.24750.0475-0.01380.3039-0.1891-0.1096-0.0451-0.0180.2616-0.2432-0.114-0.0718-19.4314106.273193.188
191.75472.38350.3453.0342.5910-0.14620.2675-0.0737-0.10130.26870.0606-0.4520.1238-0.12250.05130.094-0.029-0.14870.0226-0.277331.203858.6749173.886
201.22222.31591.65430.7982-2.48093.6449-0.0453-0.0290.05450.1437-0.20060.0813-0.40860.11930.24590.11130.0267-0.1371-0.0741-0.0063-0.11429.68161.3552174.673
215.13074.38851.4734.09871.05382.3249-0.0734-0.07190.16420.0701-0.0346-0.0722-0.461-0.43120.1080.1989-0.0098-0.1875-0.05690.0629-0.233429.478861.8251176.829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 35-177)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 178-365)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 366-414)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 35-116)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 117-156)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 157-194)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 195-340)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 341-414)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 35-115)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 116-197)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 198-365)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 366-414)
13X-RAY DIFFRACTION13(CHAIN D AND RESID 35-180)
14X-RAY DIFFRACTION14(CHAIN D AND RESID 181-364)
15X-RAY DIFFRACTION15(CHAIN D AND RESID 365-414)
16X-RAY DIFFRACTION16(CHAIN E AND RESID 2-15)
17X-RAY DIFFRACTION17(CHAIN F AND RESID 2-15)
18X-RAY DIFFRACTION18(CHAIN G AND RESID 1-14)
19X-RAY DIFFRACTION19(CHAIN H AND RESID 1-16)
20X-RAY DIFFRACTION20(CHAIN I AND RESID 1-16)
21X-RAY DIFFRACTION21(CHAIN J AND RESID 1-15)

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