PDB-5lk5: Crystal structure of the globular domain of human calreticulin mu...

ID or keywords:

Entry

Database: PDB / ID: 5lk5

Title

Crystal structure of the globular domain of human calreticulin mutant D71K

Components

Calreticulin,Calreticulin

Keywords

calcium-binding protein

Function / homology

Function and homology information

Calnexin/calreticulin cycle /

cytolytic granule / Assembly of Viral Components at the Budding Site /

cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus ...Calnexin/calreticulin cycle /

cytolytic granule / Assembly of Viral Components at the Budding Site /

cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus / intracellular glucocorticoid receptor signaling pathway / endoplasmic reticulum quality control compartment / sequestering of calcium ion / regulation of meiotic nuclear division / response to glycoside / sarcoplasmic reticulum lumen /

protein folding in endoplasmic reticulum /

hormone binding / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / cardiac muscle cell differentiation / molecular sequestering activity / Scavenging by Class A Receptors / protein maturation by protein folding / Scavenging by Class F Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / response to testosterone / cellular response to lithium ion /

smooth endoplasmic reticulum / protein localization to nucleus / negative regulation of neuron differentiation / positive regulation of cell cycle / positive regulation of phagocytosis / : / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / endocytic vesicle lumen / protein export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell migration / acrosomal vesicle / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC /

peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / intracellular calcium ion homeostasis / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / unfolded protein binding /

cellular senescence /

integrin binding /

protein folding / response to estradiol /

nuclear envelope / ER-Phagosome pathway / protein-folding chaperone binding /

spermatogenesis /

carbohydrate binding / collagen-containing extracellular matrix / regulation of apoptotic process / negative regulation of translation / protein stabilization /

ribosome / response to xenobiotic stimulus / iron ion binding /

endoplasmic reticulum lumen / external side of plasma membrane /

focal adhesion /

mRNA binding / negative regulation of DNA-templated transcription /

ubiquitin protein ligase binding /

calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II /

cell surface /

endoplasmic reticulum /

DNA binding /

extracellular space /

RNA binding / extracellular exosome / zinc ion binding / extracellular region /

membrane /

nucleus /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.3 Å

Authors

Gaboriaud, C. / Cioci, G.

Citation

Journal: IUCrJ / Year: 2016
Title: Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties.
Authors: Moreau, C. / Cioci, G. / Iannello, M. / Laffly, E. / Chouquet, A. / Ferreira, A. / Thielens, N.M. / Gaboriaud, C.

History

Deposition	Jul 21, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 31, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Dec 21, 2016	Group: Database references
Revision 1.3	Aug 1, 2018	Group: Data collection / Database references Category: citation / citation_author / pdbx_related_exp_data_set
Revision 1.4	Oct 16, 2019	Group: Data collection / Category: reflns_shell

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lk5.cif.gz	523.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5lk5.ent.gz	440.1 KB	Display	PDB format
PDBx/mmJSON format	5lk5.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/lk/5lk5 ftp://data.pdbj.org/pub/pdb/validation_reports/lk/5lk5	HTTPS FTP

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Related structure data

Related structure data	5hcaC 5hcbC 5hcfC 3pow C: citing same article (ref.)
Similar structure data	5fi0-d 3ut0-d 6ts8-d 6jxa-d 31192 6pww-d 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	#165 - Sep 2013 Designed Protein Cages similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (1)

Deposited unit

A: Calreticulin,Calreticulin

B: Calreticulin,Calreticulin

C: Calreticulin,Calreticulin

D: Calreticulin,Calreticulin

E: Calreticulin,Calreticulin

F: Calreticulin,Calreticulin

G: Calreticulin,Calreticulin

H: Calreticulin,Calreticulin

I: Calreticulin,Calreticulin

J: Calreticulin,Calreticulin

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	196.976, 196.976, 67.806
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	77
Space group name H-M	P4₂

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	18 - 367
2	1	B	18 - 367
1	2	A	19 - 366
2	2	C	19 - 366
1	3	A	18 - 367
2	3	D	18 - 367
1	4	A	19 - 366
2	4	E	19 - 366
1	5	A	19 - 366
2	5	F	19 - 366
1	6	A	19 - 366
2	6	G	19 - 366
1	7	A	19 - 365
2	7	H	19 - 365
1	8	A	19 - 367
2	8	I	19 - 367
1	9	A	19 - 366
2	9	J	19 - 366
1	10	B	19 - 367
2	10	C	19 - 367
1	11	B	18 - 367
2	11	D	18 - 367
1	12	B	19 - 365
2	12	E	19 - 365
1	13	B	19 - 367
2	13	F	19 - 367
1	14	B	19 - 367
2	14	G	19 - 367
1	15	B	19 - 366
2	15	H	19 - 366
1	16	B	19 - 366
2	16	I	19 - 366
1	17	B	19 - 367
2	17	J	19 - 367
1	18	C	19 - 366
2	18	D	19 - 366
1	19	C	19 - 366
2	19	E	19 - 366
1	20	C	19 - 367
2	20	F	19 - 367
1	21	C	19 - 367
2	21	G	19 - 367
1	22	C	19 - 365
2	22	H	19 - 365
1	23	C	19 - 367
2	23	I	19 - 367
1	24	C	19 - 367
2	24	J	19 - 367
1	25	D	19 - 366
2	25	E	19 - 366
1	26	D	19 - 366
2	26	F	19 - 366
1	27	D	19 - 366
2	27	G	19 - 366
1	28	D	19 - 365
2	28	H	19 - 365
1	29	D	19 - 367
2	29	I	19 - 367
1	30	D	19 - 366
2	30	J	19 - 366
1	31	E	19 - 366
2	31	F	19 - 366
1	32	E	19 - 366
2	32	G	19 - 366
1	33	E	19 - 366
2	33	H	19 - 366
1	34	E	19 - 365
2	34	I	19 - 365
1	35	E	19 - 366
2	35	J	19 - 366
1	36	F	19 - 367
2	36	G	19 - 367
1	37	F	19 - 365
2	37	H	19 - 365
1	38	F	19 - 367
2	38	I	19 - 367
1	39	F	19 - 367
2	39	J	19 - 367
1	40	G	19 - 365
2	40	H	19 - 365
1	41	G	19 - 367
2	41	I	19 - 367
1	42	G	19 - 367
2	42	J	19 - 367
1	43	H	19 - 366
2	43	I	19 - 366
1	44	H	19 - 365
2	44	J	19 - 365
1	45	I	19 - 367
2	45	J	19 - 367

NCS ensembles :

#1: Protein	Calreticulin,Calreticulin / CRP55 / Calregulin / Endoplasmic reticulum resident protein 60 / ERp60 / HACBP / grp60 Mass: 30160.361 Da / Num. of mol.: 10 Fragment: UNP residues 18-204,UNP residues 303-368,UNP residues 18-204,UNP residues 303-368 Mutation: D71K,D71K,D71K,D71K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALR, CRTC / Production host: Escherichia hermannii (bacteria) / References: UniProt: P27797
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 961 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.6 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG4000 0.2 M MgCl2 0.1 M Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.28→50 Å / Num. obs: 114120 / % possible obs: 95.8 % / Redundancy: 4.04 % / Net I/σ(I): 9.41

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Resolution: 2.3→47.77 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.929 / SU B: 7.387 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.26 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24685	5630	5 %	RANDOM
R_work	0.21027	-	-	-
obs	0.21211	107101	97.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 23.726 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	0 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	-0.07 Å²

Refinement step

Cycle: 1 / Resolution: 2.3→47.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20353	0	11	961	21325

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	20931
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	18756
X-RAY DIFFRACTION	r_angle_refined_deg	1.688	1.934	28172
X-RAY DIFFRACTION	r_angle_other_deg	1.664	3.001	43388
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.788	5	2520
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.553	25.709	1114
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.779	15	3525
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.78	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	2882
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	24080
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	4968
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	1.841	2.22	10161
X-RAY DIFFRACTION	r_mcbond_other	1.84	2.219	10160
X-RAY DIFFRACTION	r_mcangle_it	2.841	3.319	12631
X-RAY DIFFRACTION	r_mcangle_other	2.841	3.32	12632
X-RAY DIFFRACTION	r_scbond_it	2.713	2.472	10770
X-RAY DIFFRACTION	r_scbond_other	2.713	2.472	10771
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.303	3.598	15541
X-RAY DIFFRACTION	r_long_range_B_refined	5.964	18.02	23971
X-RAY DIFFRACTION	r_long_range_B_other	5.933	17.995	23742
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15329	0.07
1	2	B	15329	0.07
2	1	A	14485	0.11
2	2	C	14485	0.11
3	1	A	15036	0.1
3	2	D	15036	0.1
4	1	A	14398	0.12
4	2	E	14398	0.12
5	1	A	14737	0.1
5	2	F	14737	0.1
6	1	A	14828	0.11
6	2	G	14828	0.11
7	1	A	14650	0.11
7	2	H	14650	0.11
8	1	A	14505	0.12
8	2	I	14505	0.12
9	1	A	14500	0.12
9	2	J	14500	0.12
10	1	B	14414	0.11
10	2	C	14414	0.11
11	1	B	14767	0.1
11	2	D	14767	0.1
12	1	B	14482	0.12
12	2	E	14482	0.12
13	1	B	14729	0.1
13	2	F	14729	0.1
14	1	B	14776	0.1
14	2	G	14776	0.1
15	1	B	14545	0.11
15	2	H	14545	0.11
16	1	B	14487	0.11
16	2	I	14487	0.11
17	1	B	14488	0.12
17	2	J	14488	0.12
18	1	C	14581	0.11
18	2	D	14581	0.11
19	1	C	14550	0.11
19	2	E	14550	0.11
20	1	C	14816	0.1
20	2	F	14816	0.1
21	1	C	14953	0.1
21	2	G	14953	0.1
22	1	C	14558	0.11
22	2	H	14558	0.11
23	1	C	14475	0.11
23	2	I	14475	0.11
24	1	C	14825	0.1
24	2	J	14825	0.1
25	1	D	14569	0.11
25	2	E	14569	0.11
26	1	D	14867	0.1
26	2	F	14867	0.1
27	1	D	14753	0.1
27	2	G	14753	0.1
28	1	D	14637	0.1
28	2	H	14637	0.1
29	1	D	14524	0.11
29	2	I	14524	0.11
30	1	D	14667	0.11
30	2	J	14667	0.11
31	1	E	14532	0.11
31	2	F	14532	0.11
32	1	E	14558	0.12
32	2	G	14558	0.12
33	1	E	14361	0.12
33	2	H	14361	0.12
34	1	E	14589	0.12
34	2	I	14589	0.12
35	1	E	14592	0.12
35	2	J	14592	0.12
36	1	F	14950	0.1
36	2	G	14950	0.1
37	1	F	14583	0.11
37	2	H	14583	0.11
38	1	F	14469	0.11
38	2	I	14469	0.11
39	1	F	14838	0.1
39	2	J	14838	0.1
40	1	G	14733	0.11
40	2	H	14733	0.11
41	1	G	14492	0.11
41	2	I	14492	0.11
42	1	G	14970	0.1
42	2	J	14970	0.1
43	1	H	14423	0.12
43	2	I	14423	0.12
44	1	H	14773	0.11
44	2	J	14773	0.11
45	1	I	14557	0.11
45	2	J	14557	0.11

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.329	377	-
R_work	0.27	6540	-
obs	-	-	81.54 %

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