PDB-7bfi: A double-histidine mutant of HSP47 slows down client release at low pH

ID or keywords:

Entry

Database: PDB / ID: 7bfi

Title

A double-histidine mutant of HSP47 slows down client release at low pH

Components

15R8 collagen model peptide
Collagen-binding protein

Keywords

CHAPERONE / HSP47 / Collagen-binding / pH-mediated client release

Function / homology

Function and homology information

Collagen biosynthesis and modifying enzymes / negative regulation of endopeptidase activity / collagen fibril organization / collagen binding / serine-type endopeptidase inhibitor activity / endoplasmic reticulum / extracellular space
Similarity search - Function

Biological species

Canis lupus familiaris (dog)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Oecal, S. / Baumann, U.

Funding support

Germany, 1items

Citation

Journal: J.Biol.Chem. / Year: 2021
Title: Collagen's primary structure determines collagen:HSP47 complex stoichiometry.
Authors: Abraham, E.T. / Oecal, S. / Morgelin, M. / Schmid, P.W.N. / Buchner, J. / Baumann, U. / Gebauer, J.M.

History

Deposition	Jan 3, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 8, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7bfi.cif.gz	735.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7bfi.ent.gz	514 KB	Display	PDB format
PDBx/mmJSON format	7bfi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bf/7bfi ftp://data.pdbj.org/pub/pdb/validation_reports/bf/7bfi	HTTPS FTP

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Related structure data

Related structure data	7bduC 7beeC 3zhaS 4au2 4au3 4au4 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bfi-2 4au3-1 4au2-1 3zha-1 4au3-2 4eb1-d 4xsp-d 4au2-2 7jov-3 6hx4-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #53 - May 2004 Serpins similarity (9)

Deposited unit

A: Collagen-binding protein

F: 15R8 collagen model peptide

C: Collagen-binding protein

D: Collagen-binding protein

B: Collagen-binding protein

H: 15R8 collagen model peptide

I: 15R8 collagen model peptide

J: 15R8 collagen model peptide

E: 15R8 collagen model peptide

G: 15R8 collagen model peptide

186 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Collagen-binding protein

F: 15R8 collagen model peptide

B: Collagen-binding protein

E: 15R8 collagen model peptide

G: 15R8 collagen model peptide

defined by author&software
Evidence: HSP47:triple helix :HSP47
92.8 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Collagen-binding protein

D: Collagen-binding protein

H: 15R8 collagen model peptide

I: 15R8 collagen model peptide

J: 15R8 collagen model peptide

defined by author&software
92.8 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.704, 77.406, 122.343
Angle α, β, γ (deg.)	90.000, 96.602, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain "A" and (resid 36 through 123 or (resid 124...
2	1	(chain "B" and (resid 36 through 123 or (resid 124...
3	1	(chain "C" and (resid 36 through 366 or (resid 377...
4	1	(chain "D" and (resid 36 through 123 or (resid 124...
1	2	(chain "E" and resid 0 through 13)
2	2	(chain "F" and resid 0 through 13)
3	2	chain "G"
4	2	(chain "H" and resid 0 through 13)
5	2	(chain "I" and resid 0 through 13)
6	2	(chain "J" and resid 0 through 13)

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
1	1	1	LEU	PHE	A	2 - 332
1	2	1	ARG	GLY	A	336 - 370
2	1	1	LEU	PHE	F	1 - 331
2	2	1	ARG	GLY	F	333 - 367
3	1	1	LEU	PHE	D	1 - 331
3	2	1	ARG	GLY	D	342 - 376
4	1	1	LEU	GLY	E	1 - 366
1	1	2	ACE	ACE	M
1	2	2	PRO	PRO	N	2 - 14
2	1	2	ACE	ACE	B
2	2	2	PRO	PRO	C	2 - 14
3	1	2	ACE	ACE	O
3	2	2	PRO	PRO	P	2 - 14
4	1	2	ACE	ACE	G
4	2	2	PRO	PRO	H	2 - 14
5	1	2	ACE	ACE	I
5	2	2	PRO	PRO	J	2 - 14
6	1	2	ACE	ACE	K
6	2	2	PRO	PRO	L	2 - 14

NCS ensembles :

ID
1
2

#1: Protein	Collagen-binding protein / Serpin H1 Mass: 44364.773 Da / Num. of mol.: 4 / Mutation: H273N,H274N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SERPINH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2RHY7
#2: Protein/peptide	15R8 collagen model peptide Mass: 1358.547 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.85 % / Description: 100 x 50 x 50 um
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 8 % Tacsimate, 18% PEG 3350, 0.1 M HEPES, pH 7.5 / PH range: 7 - 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 22, 2016 / Details: Mirror
Radiation	Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.44→78.18 Å / Num. obs: 52937 / % possible obs: 96.9 % / Redundancy: 2.73 % / B_iso Wilson estimate: 52.85 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.069 / R_rim(I) all: 0.07 / Net I/σ(I): 11.77
Reflection shell	Resolution: 2.44→2.59 Å / Redundancy: 2.65 % / R_merge(I) obs: 0.874 / Num. unique obs: 8413 / CC_1/2: 0.635 / R_rim(I) all: 0.94 / % possible all: 95.7

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ZHA

3zha

Resolution: 2.44→78.18 Å / SU ML: 0.4199 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2482	2106	3.98 %	random
R_work	0.217	50762	-	-
obs	0.2182	52868	96.76 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 63.92 Å²

Refinement step

Cycle: LAST / Resolution: 2.44→78.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12209	0	0	104	12313

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	12486
X-RAY DIFFRACTION	f_angle_d	0.5961	16877
X-RAY DIFFRACTION	f_chiral_restr	0.0425	1862
X-RAY DIFFRACTION	f_plane_restr	0.0046	2175
X-RAY DIFFRACTION	f_dihedral_angle_d	10.5529	4709

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
1	2	A	X-RAY DIFFRACTION	Torsion NCS	0.978901923504
1	3	A	X-RAY DIFFRACTION	Torsion NCS	0.691254456844
1	4	A	X-RAY DIFFRACTION	Torsion NCS	0.836376340641
2	2	D	X-RAY DIFFRACTION	Torsion NCS	0.803171161415
2	3	D	X-RAY DIFFRACTION	Torsion NCS	0.495568283126
2	4	D	X-RAY DIFFRACTION	Torsion NCS	0.171816957093
2	5	D	X-RAY DIFFRACTION	Torsion NCS	0.730900344739
2	6	D	X-RAY DIFFRACTION	Torsion NCS	0.369355294705

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.44-2.5	0.4398	135	0.4041	3242	X-RAY DIFFRACTION	92.52
2.5-2.56	0.3524	139	0.3429	3379	X-RAY DIFFRACTION	97.61
2.56-2.63	0.3733	138	0.3242	3393	X-RAY DIFFRACTION	97.62
2.63-2.71	0.3846	141	0.3039	3390	X-RAY DIFFRACTION	97.81
2.71-2.79	0.2989	142	0.2881	3382	X-RAY DIFFRACTION	97.75
2.79-2.89	0.3181	143	0.2831	3386	X-RAY DIFFRACTION	97.41
2.89-3.01	0.35	140	0.2767	3392	X-RAY DIFFRACTION	97.46
3.01-3.15	0.3632	140	0.2807	3424	X-RAY DIFFRACTION	97.3
3.15-3.31	0.286	132	0.242	3325	X-RAY DIFFRACTION	96.19
3.31-3.52	0.2293	142	0.2187	3391	X-RAY DIFFRACTION	96.61
3.52-3.79	0.2611	141	0.2233	3412	X-RAY DIFFRACTION	97.91
3.79-4.17	0.244	143	0.1938	3426	X-RAY DIFFRACTION	97.81
4.17-4.78	0.1896	142	0.1568	3437	X-RAY DIFFRACTION	97.44
4.78-6.02	0.205	145	0.1808	3404	X-RAY DIFFRACTION	96.31
6.02-78.18	0.1679	143	0.1685	3379	X-RAY DIFFRACTION	93.79

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.40196942321	0.339651206513	1.06498148072	2.30234805439	-0.798801632241	4.29856934416	-0.240491023577	0.119621043859	-0.0842617237751	-0.0686227268947	0.07431831023	-0.0992628139936	-0.414650461209	-0.01534983302	-0.000240353022711	0.413844372912	-0.0376854158528	0.0115936082104	0.338344979817	-0.0134726141817	0.398058959467	25.604612485	40.1423918311	-128.125937337
2	1.45631706148	0.0113896815941	0.77950818395	1.83724064125	-0.163301561041	4.76478201921	-0.106549232225	-0.118110421633	-0.0747766673063	0.250398945719	0.242780540368	0.0263501426249	0.0834511558575	-0.000493783910477	0.0090530235689	0.403106196219	0.0296318050386	0.0334442116167	0.328313333652	0.00763370655614	0.395049862342	27.0237588615	36.500170525	-107.249421832
3	1.43846294313	-0.286491095183	0.363744220592	1.62501555102	0.121117367785	3.53731267644	-0.124986459696	-0.0460689440691	-0.128355695276	0.144506740351	0.20478449845	0.0195768846513	-0.0503119588839	-0.160545863561	0.000107855152819	0.329902567987	0.00867387104891	0.0379445340968	0.400751640693	0.00239410197683	0.397254694195	24.1206855792	36.60301778	-114.449177786
4	1.60849047112	-0.730147193845	0.154364152748	1.58434664947	1.15837301088	2.61543667893	0.0704119292313	0.32444507122	-0.0588478811504	-0.129113655156	-0.0151811228299	-0.0505214877183	0.679815612706	-0.398696441464	-0.00662484634966	0.579782609028	-0.116710902421	0.0756705979824	0.364001538868	-0.00206230556604	0.44390757895	16.8782440993	13.9105119937	-49.3009147648
5	1.72888593693	-0.207348122788	-0.796569929856	0.660451263564	0.232776524504	4.41695913856	-0.01425296084	-0.0928711432163	0.042428573595	0.0573794651078	-0.0680900433689	0.130051665325	-0.0122732529045	-0.386968621069	0.00143113859287	0.323053290942	0.0137134678927	-0.014142640576	0.277526529988	-0.0322134815964	0.444131335625	20.3004332574	25.7744991174	-55.4616142153
6	1.65149016482	-0.0659222057518	-0.651162079566	0.419237293861	1.04881708729	2.98394358173	-0.0127002369719	0.0589772671271	-0.0349008654575	-0.152038027194	-0.122117233977	-0.131120933168	0.135836540293	0.080692420197	-0.00149714598984	0.392043266281	0.0458956054805	0.0207761211072	0.264893692011	0.0435833852663	0.407450917952	21.3870292797	25.8479302546	-60.2576287604
7	1.28569692061	1.05134566432	0.0607656133113	1.59294750272	-0.319064082277	1.503045519	-0.294299477907	0.353409110893	0.21423744682	-0.414218251652	0.206514353025	0.116898487675	-0.237781301463	0.207695003512	0.000274079213097	0.581113142739	-0.0645609313242	-0.0425226931132	0.786275224193	0.0794616942596	0.4969267174	42.7397880233	9.10004954271	-130.347243571
8	1.70678661109	-0.0413614593017	1.04931046797	1.33879213804	0.363440257123	4.68346591445	-0.032629112853	0.320133769412	-0.0196138707272	0.085543820619	0.0402809514211	0.051338107157	0.285008638236	0.377324090287	0.00115172593375	0.43183451255	0.0280647683199	0.00182148127882	0.537198434535	0.00773217412878	0.479209799916	41.4499878146	0.154616129792	-119.804323169
9	1.13718475443	-0.298502446475	0.27741319506	0.395310042666	0.507734848718	1.03798591709	-0.207964776002	0.0392764266745	0.334749468651	0.479256180198	0.168089966453	-0.223057356783	0.0167719656209	0.928124308965	0.00437064494832	0.575998212156	0.0156261693002	-0.0959907550189	0.754807015024	-0.0308808973812	0.5140923803	50.6428337041	4.91984116854	-105.611409966
10	1.5374886188	0.125183381082	-1.07808951218	0.564218879017	-0.0628638843586	1.46446442321	-0.168236112033	-0.209592174291	-0.542245426463	-0.178856861489	0.124605358077	0.521996926322	0.331609747952	-0.606396459265	0.000614660183641	0.441425565927	0.000278920404428	0.0692311606921	0.613714614776	0.105359658793	0.709503303617	26.9062677351	-20.9326537234	-54.3502158957
11	2.4596141671	-0.145073430237	-0.173330550398	1.80883370415	-0.177724624333	2.75742165336	-0.0218747528879	-1.2351364038	-0.414988088486	0.0610990795357	-0.0339243547231	-0.422196745261	-0.216311112482	0.287568714642	0.137878495023	0.459778004306	0.0604650337812	-0.0509541951831	0.690011479738	0.162418705545	0.481742270635	39.1768773234	-11.3997365606	-45.7702790971
12	2.94688148919	0.0217309347744	-0.925730426717	0.948925539261	-0.235244967133	2.86964274958	-0.0483014074747	-0.0317448278001	-0.119609977111	-0.183590035336	-0.0124497596174	0.116330092935	0.0590690214322	-0.202790102585	0.00229814596406	0.377450549089	0.0860133847741	-0.0541126224514	0.370303389407	-0.0151482142422	0.474631530079	34.0395040132	-10.2394479761	-68.8533385359
13	0.408340697811	0.576473845062	0.149742518089	0.796074028836	0.13878890416	1.0649094138	0.195226372308	0.342692116452	0.560701317099	-0.328436085292	-0.0316977687765	-0.287267618836	-0.142198626464	0.200404206346	0.000544848191156	0.450189940575	0.152171783765	0.0332883759561	0.580496145083	0.055379932658	0.448611758311	24.3103538591	37.2164928132	-84.0309910619
14	0.196795334451	0.417257790333	0.0684918910388	0.862583409016	0.0629354638456	1.56146502267	0.379268268992	0.705216628501	0.063093963897	-0.482003906257	-0.276389822779	-0.00306562484725	-0.253666861364	0.165343325188	0.00452711974681	0.468339493074	0.183678511854	-0.016060300433	0.533601751051	0.0257027386982	0.504621176959	40.277051581	2.33263978198	-88.677025023

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID	End label seq-ID
1	1	(chain A and resid 36:159)	A	A	36 - 159	2 - 125
2	2	(chain A and resid 160:305)	A	A	160 - 305	126 - 271
3	3	(chain A and resid 306:413)	A	A	306 - 413	272 - 372
4	4	(chain B and resid 36:126)	B	F	36 - 126	1 - 91
5	5	(chain B and resid 127:340)	B	F	127 - 340	92 - 305
6	6	(chain B and resid 341:413)	B	F	341 - 413	306 - 369
7	7	(chain C and resid 36:126)	C	D	36 - 126	1 - 91
8	8	(chain C and resid 127:365)	C	D	127 - 365	92 - 330
9	9	(chain C and resid 366:411)	C	D	366 - 411	331 - 376
10	10	(chain D and resid 36:113)	D	E	36 - 113	1 - 78
11	11	(chain D and resid 114:204)	D	E	114 - 204	79 - 169
12	12	(chain D and resid 205:412)	D	E	205 - 412	170 - 367
13	13	(chain E or chain F or chain G)	F - G	B - P	0 - 13		14
14	14	(chain H or chain I or chain J )	H - J	G - L	0 - 14		15

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