PDB-9h0c: Crystal structure of BiP ATPase domain in complex with CDNF C-ter...

ID or keywords:

Entry

Database: PDB / ID: 9h0c

Title

Crystal structure of BiP ATPase domain in complex with CDNF C-terminal domain at 1.65 angstroms resolution

Components

Cerebral dopamine neurotrophic factor
Endoplasmic reticulum chaperone BiP

Keywords

CHAPERONE / Endoplasmic reticulum Chaperone Neurotrophic factor Unfolded protein response

Function / homology

Function and homology information

regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response ...regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / negative regulation of IRE1-mediated unfolded protein response / PERK regulates gene expression / protein folding in endoplasmic reticulum / cerebellar Purkinje cell layer development / misfolded protein binding / dopaminergic neuron differentiation / post-translational protein targeting to membrane, translocation / Modulation of host responses by IFN-stimulated genes / ER overload response / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of PERK-mediated unfolded protein response / non-chaperonin molecular chaperone ATPase / : / protein serine/threonine kinase inhibitor activity / Regulation of HSF1-mediated heat shock response / negative regulation of protein-containing complex assembly / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / heat shock protein binding / ERAD pathway / protein folding chaperone / substantia nigra development / cellular response to interleukin-4 / response to endoplasmic reticulum stress / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / growth factor activity / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / neuron projection development / unfolded protein binding / melanosome / Platelet degranulation / protein-folding chaperone binding / ribosome binding / protein refolding / midbody / positive regulation of cell migration / cadherin binding / endoplasmic reticulum lumen / protein domain specific binding / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / extracellular exosome / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Fudo, S. / Shpironok, O. / Saarma, M. / Kajander, T.

Funding support

Finland, 1items

Citation

Journal: To Be Published
Title: Molecular basis for CDNF function in BiP chaperone cycle regulation
Authors: Fudo, S. / Shpironok, O. / Saarma, M. / Kajander, T.

History

Deposition	Oct 8, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9h0c.cif.gz	186.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9h0c.ent.gz	146.6 KB	Display	PDB format
PDBx/mmJSON format	9h0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9h0c_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	9h0c_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9h0c_validation.xml.gz	24.1 KB	Display
Data in CIF	9h0c_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h0/9h0c ftp://data.pdbj.org/pub/pdb/validation_reports/h0/9h0c	HTTPS FTP

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Related structure data

Similar structure data	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 (9) #55 - Jul 2004 DNA Ligase similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #213 - Sep 2017 Sirtuins similarity (1)

Deposited unit

A: Endoplasmic reticulum chaperone BiP

B: Cerebral dopamine neurotrophic factor

hetero molecules

49.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, fluorescence resonance energy transfer, surface plasmon resonance

Unit cell

Length a, b, c (Å)	50.522, 80.612, 102.349
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 2 types, 2 molecules AB

#1: Protein	Endoplasmic reticulum chaperone BiP / 78 kDa glucose-regulated protein / GRP-78 / Binding-immunoglobulin protein / BiP / Heat shock ...78 kDa glucose-regulated protein / GRP-78 / Binding-immunoglobulin protein / BiP / Heat shock protein 70 family protein 5 / HSP70 family protein 5 / Heat shock protein family A member 5 / Immunoglobulin heavy chain-binding protein Mass: 42098.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Production host: Escherichia coli (E. coli) References: UniProt: P11021, non-chaperonin molecular chaperone ATPase
#2: Protein	Cerebral dopamine neurotrophic factor / ARMET-like protein 1 / Conserved dopamine neurotrophic factor Mass: 7059.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q49AH0

#1: Protein

Endoplasmic reticulum chaperone BiP / 78 kDa glucose-regulated protein / GRP-78 / Binding-immunoglobulin protein / BiP / Heat shock ...

Mass: 42098.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: HSPA5, GRP78 / Production host:

Escherichia coli (E. coli)
References: UniProt: P11021, non-chaperonin molecular chaperone ATPase

#2: Protein

Cerebral dopamine neurotrophic factor / ARMET-like protein 1 / Conserved dopamine neurotrophic factor

Mass: 7059.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.)

Homo sapiens (human) / References: UniProt: Q49AH0

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Non-polymers , 5 types, 365 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 200 mM NaCl, 25% (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 1.65→40.31 Å / Num. obs: 50649 / % possible obs: 99.2 % / Redundancy: 4.3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.108 / R_pim(I) all: 0.058 / R_rim(I) all: 0.123 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.65→1.678 Å / Redundancy: 3.6 % / R_merge(I) obs: 1.129 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2315 / CC_1/2: 0.431 / R_pim(I) all: 0.671 / R_rim(I) all: 1.32 / % possible all: 92.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→40.31 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.959 / SU B: 4.776 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2026	2434	4.8 %	RANDOM
R_work	0.18051	-	-	-
obs	0.18161	48172	99.09 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	-0 Å²	0 Å²
2-	-	0.02 Å²	-0 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: 1 / Resolution: 1.65→40.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3250	0	13	361	3624

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	3339
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3100
X-RAY DIFFRACTION	r_angle_refined_deg	1.464	1.647	4513
X-RAY DIFFRACTION	r_angle_other_deg	0.504	1.565	7231
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.867	5	425
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.249	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.953	10	594
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	514
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3811
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	621
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.14	1.084	1697
X-RAY DIFFRACTION	r_mcbond_other	1.14	1.084	1697
X-RAY DIFFRACTION	r_mcangle_it	1.884	1.618	2123
X-RAY DIFFRACTION	r_mcangle_other	1.883	1.618	2124
X-RAY DIFFRACTION	r_scbond_it	1.951	1.371	1642
X-RAY DIFFRACTION	r_scbond_other	1.951	1.371	1642
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.02	1.95	2391
X-RAY DIFFRACTION	r_long_range_B_refined	6.145	20.641	3753
X-RAY DIFFRACTION	r_long_range_B_other	6.072	17.94	3668
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	162	-
R_work	0.303	3272	-
obs	-	-	92.61 %

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	1.7084	0.6285	-1.0197	0.9146	-1.3415	4.885	0.082	-0.2763	-0.0858	-0.0475	-0.0805	0.018	0.1106	0.1483	-0.0016	0.051	-0.0169	-0.0004	0.0455	0.0119	0.2521	28.286	58.633	38.248
2	1.1363	-0.1597	0.2438	0.4038	0.2425	0.7198	0.0426	0.1024	0.0038	-0.1251	-0.0346	0.0302	-0.0039	-0.0257	-0.0081	0.0684	0.0009	-0.0194	0.0137	-0.0036	0.262	24.068	64.402	18.814
3	1.1591	0.1147	0.2578	0.6046	-0.0826	0.6802	0.0089	-0.1248	0.0815	0.0275	-0.0217	0.0828	-0.0106	-0.0922	0.0127	0.0587	0.0002	0.0088	0.0209	-0.0142	0.2724	23.446	66.591	31.363
4	0.8524	-0.01	0.556	0.5129	1.2784	3.9835	-0.0044	-0.1022	-0.0084	-0.0588	-0.0006	-0.0552	-0.1197	-0.0824	0.005	0.0501	-0.005	-0.0036	0.0134	0.0061	0.2427	43.992	67.649	32.266
5	2.975	0.3283	1.8066	1.2593	0.1753	3.6568	0.0148	0.1676	-0.1657	0.0221	0.0566	-0.0292	0.0396	-0.21	-0.0714	0.0255	0.0009	0.0079	0.0509	-0.033	0.2247	37.729	48.171	7.734
6	1.1818	0.0901	0.7434	0.6886	0.9364	1.6091	-0.0021	0.0102	-0.0149	-0.0077	0.0691	-0.0469	0.0051	0.0962	-0.067	0.0823	-0.0058	0.0025	0.0091	0.0045	0.3144	51.842	63.907	26.403
7	4.9864	0.3252	-1.2327	0.1551	0.3257	1.5717	0.1205	-0.2819	-0.195	0.0696	-0.0489	-0.0695	0.1334	-0.0221	-0.0716	0.0918	-0.0072	-0.0179	0.0269	0.0395	0.2754	42.824	59.559	37.275
8	25.1448	-9.3776	18.1346	18.3782	-11.7439	14.7763	-0.1957	0.0189	0.7764	-0.5171	-0.5015	-0.5639	0.0135	0.1985	0.6972	0.2947	-0.236	0.2619	0.3073	-0.3383	0.589	43.441	85.119	48.584
9	17.5979	-3.6367	-9.3085	4.5067	0.0634	24.1839	-0.0696	-1.1462	0.897	0.222	0.7144	-0.5723	-0.0856	0.8058	-0.6448	0.0118	0.0313	-0.0269	0.1699	-0.1832	0.2781	41.124	79.884	55.329
10	28.5003	0.3611	-6.8015	8.1399	5.1557	9.1722	-0.544	-0.7405	-0.4881	0.3918	0.4109	-0.0208	0.3234	0.3273	0.1331	0.0378	0.047	0.0307	0.3195	-0.0615	0.19	33.055	79.543	59.773
11	15.1482	-10.0082	-14.4988	9.249	11.7924	28.3896	-0.7135	-0.1163	-0.7305	0.7269	-0.0193	0.3929	1.0263	-0.8675	0.7329	0.1342	-0.0065	0.0988	0.1136	-0.013	0.3035	31.692	71.627	50.914
12	14.6484	-5.6968	-10.7111	8.7911	5.3489	11.7861	0.4538	-0.1496	0.3753	-0.3726	-0.0008	-0.1256	-0.5566	-0.0807	-0.4531	0.032	0.0088	0.0215	0.0259	-0.0261	0.2342	35.55	78.857	46.601
13	27.8754	-3.4979	-6.8954	5.2396	5.2896	29.4071	-0.1568	-0.4333	0.3354	-0.1817	0.1856	-0.057	-1.4422	-0.3392	-0.0287	0.1193	0.0705	0.0026	0.0881	-0.0692	0.2841	28.716	85.453	54.412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	27 - 49
2	X-RAY DIFFRACTION	2	A	50 - 126
3	X-RAY DIFFRACTION	3	A	127 - 211
4	X-RAY DIFFRACTION	4	A	212 - 261
5	X-RAY DIFFRACTION	5	A	262 - 327
6	X-RAY DIFFRACTION	6	A	328 - 376
7	X-RAY DIFFRACTION	7	A	377 - 405
8	X-RAY DIFFRACTION	8	B	113 - 117
9	X-RAY DIFFRACTION	9	B	118 - 124
10	X-RAY DIFFRACTION	10	B	125 - 130
11	X-RAY DIFFRACTION	11	B	131 - 136
12	X-RAY DIFFRACTION	12	B	137 - 144
13	X-RAY DIFFRACTION	13	B	145 - 152

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