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- PDB-3zha: Molecular basis for the action of the collagen-specific chaperone... -

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Basic information

Entry
Database: PDB / ID: 3zha
TitleMolecular basis for the action of the collagen-specific chaperone Hsp47 SERPINH1 and its structure-specific client recognition.
Components
  • COLLAGEN MODEL PEPTIDE 18-T8R11
  • HSP47
KeywordsCHAPERONE / COLLAGEN
Function / homology
Function and homology information


Collagen biosynthesis and modifying enzymes / negative regulation of endopeptidase activity / collagen trimer / collagen fibril organization / collagen binding / serine-type endopeptidase inhibitor activity / endoplasmic reticulum lumen / endoplasmic reticulum / extracellular space
Similarity search - Function
Serpin H1 / 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 H1 / 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
SUCCINIC ACID / Serpin H1 / Collagen-binding protein
Similarity search - Component
Biological speciesCANIS LUPUS FAMILIARIS (dog)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWidmer, C. / Gebauer, J.M. / 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
DepositionDec 20, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionJan 9, 2013ID: 4AWR
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HSP47
B: HSP47
C: HSP47
D: HSP47
E: COLLAGEN MODEL PEPTIDE 18-T8R11
F: COLLAGEN MODEL PEPTIDE 18-T8R11
G: COLLAGEN MODEL PEPTIDE 18-T8R11
H: COLLAGEN MODEL PEPTIDE 18-T8R11
I: COLLAGEN MODEL PEPTIDE 18-T8R11
J: COLLAGEN MODEL PEPTIDE 18-T8R11
K: HSP47
L: HSP47
M: COLLAGEN MODEL PEPTIDE 18-T8R11
N: COLLAGEN MODEL PEPTIDE 18-T8R11
O: COLLAGEN MODEL PEPTIDE 18-T8R11
P: HSP47
Q: HSP47
R: COLLAGEN MODEL PEPTIDE 18-T8R11
S: COLLAGEN MODEL PEPTIDE 18-T8R11
T: COLLAGEN MODEL PEPTIDE 18-T8R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,54125
Polymers372,95120
Non-polymers5905
Water3,999222
1
A: HSP47
B: HSP47
E: COLLAGEN MODEL PEPTIDE 18-T8R11
F: COLLAGEN MODEL PEPTIDE 18-T8R11
G: COLLAGEN MODEL PEPTIDE 18-T8R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3566
Polymers93,2385
Non-polymers1181
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-52.6 kcal/mol
Surface area32380 Å2
MethodPISA
2
P: HSP47
Q: HSP47
R: COLLAGEN MODEL PEPTIDE 18-T8R11
S: COLLAGEN MODEL PEPTIDE 18-T8R11
T: COLLAGEN MODEL PEPTIDE 18-T8R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4747
Polymers93,2385
Non-polymers2362
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-44.3 kcal/mol
Surface area32760 Å2
MethodPISA
3
C: HSP47
D: HSP47
H: COLLAGEN MODEL PEPTIDE 18-T8R11
I: COLLAGEN MODEL PEPTIDE 18-T8R11
J: COLLAGEN MODEL PEPTIDE 18-T8R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3566
Polymers93,2385
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-46.7 kcal/mol
Surface area32620 Å2
MethodPISA
4
K: HSP47
L: HSP47
M: COLLAGEN MODEL PEPTIDE 18-T8R11
N: COLLAGEN MODEL PEPTIDE 18-T8R11
O: COLLAGEN MODEL PEPTIDE 18-T8R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3566
Polymers93,2385
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-44.1 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.709, 104.905, 171.840
Angle α, β, γ (deg.)90.00, 103.71, 90.00
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 44283.680 Da / Num. of mol.: 8 / Fragment: RESIDUES 36-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANIS LUPUS FAMILIARIS (dog) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: C7C419, UniProt: E2RHY7*PLUS
#2: Protein/peptide
COLLAGEN MODEL PEPTIDE 18-T8R11


Mass: 1556.765 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsACETYL GROUP (ACE): ACETYLATED AMINO TERMINUS
Sequence detailsDISORDERED SIDE CHAINS MODELLED AS ALA,GLY

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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: 2.41 Å3/Da / Density % sol: 50 % / 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: DECTRIS PILATUS / Detector: PIXEL / Date: Jun 6, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 113422 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 51.12 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.1
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 0.94 / % possible all: 94.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AU2

4au2


Resolution: 2.55→49.16 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9315 / SU R Cruickshank DPI: 0.672 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.567 / SU Rfree Blow DPI: 0.251 / SU Rfree Cruickshank DPI: 0.261
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1780 1.57 %RANDOM
Rwork0.1952 ---
obs0.1956 113420 98.03 %-
Displacement parametersBiso mean: 58.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.1093 Å20 Å20.0861 Å2
2--6.2526 Å20 Å2
3----6.1433 Å2
Refine analyzeLuzzati coordinate error obs: 0.387 Å
Refinement stepCycle: LAST / Resolution: 2.55→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24641 0 40 222 24903
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00925257HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1434132HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8749SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes539HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3651HARMONIC5
X-RAY DIFFRACTIONt_it25257HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3172SEMIHARMONIC5
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_contact27360SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 132 1.66 %
Rwork0.2414 7797 -
all0.2414 7929 -
obs--98.03 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined4.0630.58470.65284.388-0.79571.8355-0.35290.4677-0.1398-0.77150.30070.8730.1598-0.2230.05210.1583-0.0926-0.17090.1797-0.02260.1867-62.2493-130.681-190.3748
2refined2.20340.42220.54562.83990.52161.1893-0.14790.02850.0788-0.3560.06660.3972-0.1743-0.08810.08140.08650.001-0.09540.09560.01110.0893-49.59-116.942-183.2844
3refined4.94090.61280.19282.09930.78034.08120.043-0.77260.14260.20380.0469-0.2532-0.09410.7152-0.08990.0831-0.0358-0.00980.3865-0.09740.1393-8.3084-88.5114-138.6249
4refined1.66650.3452-0.26881.36310.97231.92540.0851-0.27390.06880.23120.0077-0.04110.08130.1669-0.09280.04640.0035-0.0220.2-0.01130.1118-22.718-95.7892-149.6945
5refined2.1477-0.55870.23264.4036-0.16521.2860.14690.147-0.3262-0.7688-0.13661.37410.044-0.3791-0.01030.29990.0539-0.31850.2582-0.13010.7501-82.495-119.688-106.7578
6refined-70.9271-106.052-101.1136
7refined1.9254-0.6382-0.06583.42030.09360.4236-0.02030.1439-0.1498-0.4826-0.02520.6367-0.134-0.15740.04550.20120.0327-0.12530.171-0.06520.2657-63.3599-102.335-100.077
8refined2.58860.48210.24734.48490.95581.95850.13990.13650.0603-0.5502-0.1332-0.1325-0.08980.0606-0.00680.18590.0737-0.08470.1252-0.01310.1894-34.0897-83.7474-50.8359
9refined2.61630.6198-1.00650.81540.17333.06670.0853-0.763-0.46150.3335-0.10750.03060.09640.64920.02230.3074-0.0332-0.01060.53640.06420.1963-22.9785-71.4065-60.2727
10refined4.49030.58380.04042.484-1.74725.14310.0038-0.25010.82560.22330.1255-0.2992-0.7150.8821-0.12930.2154-0.193-0.02370.4571-0.07040.1983-42.9291-84.6834-66.5053
11refined1.41510.36760.04121.29411.24342.63020.0658-0.2984-0.01610.2870.0088-0.02810.0010.1999-0.07450.18460.0040.00190.22890.03260.1679-45.1472-89.6458-72.3473
12refined4.95071.31452.23710.40591.912.33190.0588-0.028-0.3479-0.02360.1314-0.27170.20230.3579-0.19010.16280.0090.03340.2509-0.00490.2088-32.4376-105.918-172.4381
13refined-0.71052.0441.99261.75750.71283.3299-0.0821-0.13820.2705-0.47660.1517-0.2438-0.28630.0292-0.06960.1604-0.08670.00390.189-0.06630.2451-32.5374-103.628-172.8526
14refined2.24223.4393.1073.8221-0.63131.4099-0.00390.3615-0.2873-0.2075-0.03720.3296-0.2799-0.08720.04110.1381-0.0765-0.08110.24250.06090.0824-32.4012-103.009-170.1585
15refined1.25982.79010.67071.28610.92952.63490.0486-0.0376-0.19970.0962-0.0890.2692-0.2511-0.09180.04040.1123-0.023-0.00880.2305-0.00940.1547-52.7494-94.7752-89.2739
16refined1.88892.70781.59450.8047-1.9392.09480.1926-0.0270.258-0.16670.0209-0.1056-0.1457-0.0341-0.21350.098-0.0535-0.00770.2067-0.06390.2356-52.8905-92.4957-89.7846
17refined1.81940.83992.01514.4217-0.92820.8749-0.03710.0475-0.1483-0.03120.05990.0189-0.33520.0282-0.02280.0705-0.0537-0.07680.0935-0.0660.104-52.7448-91.8842-87.0401
18refined0.20123.9970.78321.74431.32.55750.1662-0.2493-0.1948-0.1622-0.07920.2731-0.1821-0.016-0.0870.1350.03380.00760.17360.02130.2203-14.0818-28.91-192.4508
19refined4.1250.2354-0.54282.97531.5471.7501-0.12390.21760.2872-0.43970.3536-0.4947-0.27470.363-0.22970.0957-0.06910.11330.2146-0.03670.1379-25.4708-44.4088-188.0899
20refined2.72330.478-0.50911.70610.50480.99960.00180.0556-0.0515-0.11580.0723-0.29310.09690.2901-0.07410.06540.02010.04660.1630.00080.0114-33.2838-47.3335-186.6671
21refined5.93421.33580.84612.8188-0.13823.1892-0.0709-0.05610.098-0.10930.11490.10850.09280.0443-0.0440.0201-0.00640.08250.0436-0.0187-0.055-58.8715-72.6492-136.7256
22refined4.18240.71781.15553.2751-0.20072.36490.4231-1.3346-0.18110.73-0.22610.40850.1943-0.7898-0.1970.1831-0.13910.06540.61770.0934-0.0209-50.5441-68.5052-156.7351
23refined2.4417-0.26610.32740.994-0.91862.09950.1699-0.1333-0.1066-0.0708-0.0574-0.02290.24350.0509-0.11250.1183-0.0195-0.020.1620.00720.1085-48.3556-69.9823-148.1158
24refined3.76910.53110.75121.6514-0.83362.5280.2655-0.7969-0.22380.3172-0.1576-0.10340.108-0.1441-0.10790.0921-0.028-0.02430.24330.0325-0.0073-41.4046-56.0352-175.3843
25refined-0.22641.9247-0.0321.8256-0.41014.06560.0214-0.15620.0867-0.10780.01220.18730.23480.3443-0.03360.0742-0.01080.07420.12740.03170.0256-40.1008-59.2391-175.621
26refined2.4658-1.9115-5.2092.1141.52751.2735-0.0495-0.04150.004-0.0118-0.1016-0.28140.53960.26790.15110.11020.06820.03050.1777-0.02740.121-38.7837-61.1214-173.309
27refined-1.65493.21773.95491.1563-3.49893.8035-0.04530.1301-0.5590.2309-0.0114-0.29990.33820.42290.05670.06960.07930.12190.21880.00120.0905-34.0047-19.2057-114.1034
28refined6.18211.552-2.32635.21850.40112.88750.00171.02590.1823-0.91610.2428-1.1054-0.20280.0264-0.24460.26080.01150.20290.3994-0.04770.4255-43.375-30.0092-102.6862
29refined2.96971.10960.08372.61070.28071.0732-0.0765-0.0447-0.2194-0.15860.1228-0.55720.19720.249-0.04630.16950.08630.03960.17880.01350.3203-47.7036-30.1518-103.8248
30refined5.3111.5837-0.75473.6197-0.11211.16490.05720.10240.1471-0.18060.1042-0.30730.13120.0731-0.16140.22570.04970.03270.21460.02530.2175-78.3255-61.773-53.0769
31refined3.76840.0031.33152.68120.58972.72030.1398-1.0953-0.12880.2397-0.05670.28210.2024-0.5402-0.08320.1749-0.03410.08390.40220.04350.0704-68.3358-55.7415-72.4899
32refined2.131-0.2740.39311.5387-1.21161.96530.0318-0.20280.12880.1019-0.0814-0.05570.08730.10060.04970.21790.0195-0.01250.1479-0.04980.2315-71.5505-62.3723-63.7335
33refined2.49820.57590.30291.0545-1.03312.51630.1359-0.4901-0.30350.2632-0.03110.03310.1449-0.2292-0.10480.26130.00760.02440.20940.03460.222-61.5558-44.9316-92.4497
34refined-0.0831.5681-0.45693.3670.71495.1410.06460.03670.1682-0.25350.0190.04630.06970.1712-0.08360.0837-0.08940.01650.21040.11180.1965-61.58-47.3535-93.1854
35refined1.98842.1314-2.94810.54080.27060.5423-0.0854-0.14190.1068-0.0105-0.07870.10750.10580.16510.16410.1660.01470.01480.28510.05150.1539-60.1827-49.0528-90.3957
36-1.9214.00933.42311.8565-3.50824.21470.1526-0.0915-0.1029-0.1238-0.0894-0.02630.0540.2106-0.06320.22070.05280.08940.2640.08560.1834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 35-186
2X-RAY DIFFRACTION2CHAIN A AND RESID 187-416
3X-RAY DIFFRACTION3CHAIN B AND RESID 35-204
4X-RAY DIFFRACTION4CHAIN B AND RESID 205-365
5X-RAY DIFFRACTION5CHAIN C AND RESID 36-195
6X-RAY DIFFRACTION6CHAIN C AND RESID 196-366
7X-RAY DIFFRACTION7CHAIN C AND RESID 367-414
8X-RAY DIFFRACTION8CHAIN D AND RESID 35-120
9X-RAY DIFFRACTION9CHAIN D AND RESID 126-203
10X-RAY DIFFRACTION10CHAIN D AND RESID 204-364
11X-RAY DIFFRACTION11CHAIN D AND RESID 365-412
12X-RAY DIFFRACTION12CHAIN E AND RESID 0-17
13X-RAY DIFFRACTION13CHAIN F AND RESID 0-16
14X-RAY DIFFRACTION14CHAIN G AND RESID 0-15
15X-RAY DIFFRACTION15CHAIN H AND RESID 0-17
16X-RAY DIFFRACTION16CHAIN I AND RESID 1-16
17X-RAY DIFFRACTION17CHAIN J AND RESID 0-15
18X-RAY DIFFRACTION18CHAIN K AND RESID 35-207
19X-RAY DIFFRACTION19CHAIN K AND RESID 208-366
20X-RAY DIFFRACTION20CHAIN K AND RESID 367-414
21X-RAY DIFFRACTION21CHAIN L AND RESID 35-166
22X-RAY DIFFRACTION22CHAIN L AND RESID 167-276
23X-RAY DIFFRACTION23CHAIN L AND RESID 277-414
24X-RAY DIFFRACTION24CHAIN M AND RESID 1-17
25X-RAY DIFFRACTION25CHAIN N AND RESID 1-17
26X-RAY DIFFRACTION26CHAIN O AND RESID 1-17
27X-RAY DIFFRACTION27CHAIN P AND RESID 37-158
28X-RAY DIFFRACTION28CHAIN P AND RESID 159-339
29X-RAY DIFFRACTION29CHAIN P AND RESID 340- 414
30X-RAY DIFFRACTION30CHAIN Q AND RESID 35-165
31X-RAY DIFFRACTION31CHAIN Q AND RESID 166-311
32X-RAY DIFFRACTION32CHAIN Q AND RESID 312-411
33X-RAY DIFFRACTION33CHAIN R AND RESID 0-16
34X-RAY DIFFRACTION34CHAIN S AND RESID 0-16
35X-RAY DIFFRACTION35CHAIN T AND RESID 0-16

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