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

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Basic information

Entry
Database: PDB / ID: 5lk5
TitleCrystal structure of the globular domain of human calreticulin mutant D71K
ComponentsCalreticulin,Calreticulin
Keywordscalcium-binding protein
Function / homology
Function and homology information


Calnexin/calreticulin cycle / response to biphenyl / cytolytic granule / positive regulation of dendritic cell chemotaxis / ATF6 (ATF6-alpha) activates chaperone genes / nuclear receptor-mediated glucocorticoid signaling pathway / Assembly of Viral Components at the Budding Site / cortical granule / negative regulation of trophoblast cell migration / complement component C1q complex binding ...Calnexin/calreticulin cycle / response to biphenyl / cytolytic granule / positive regulation of dendritic cell chemotaxis / ATF6 (ATF6-alpha) activates chaperone genes / nuclear receptor-mediated glucocorticoid signaling pathway / Assembly of Viral Components at the Budding Site / cortical granule / negative regulation of trophoblast cell migration / complement component C1q complex binding / response to peptide / cellular response to electrical stimulus / regulation of meiotic nuclear division / sequestering of calcium ion / negative regulation of retinoic acid receptor signaling pathway / endoplasmic reticulum quality control compartment / protein folding in endoplasmic reticulum / sarcoplasmic reticulum lumen / hormone binding / negative regulation of intracellular steroid hormone receptor signaling pathway / nuclear export signal receptor activity / cardiac muscle cell differentiation / response to glycoside / cortical actin cytoskeleton organization / Scavenging by Class A Receptors / nuclear androgen receptor binding / Scavenging by Class F Receptors / cellular response to lithium ion / response to testosterone / molecular sequestering activity / negative regulation of neuron differentiation / protein localization to nucleus / smooth endoplasmic reticulum / positive regulation of cell cycle / positive regulation of phagocytosis / ERAD pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / endocytic vesicle lumen / positive regulation of substrate adhesion-dependent cell spreading / peptide binding / protein folding chaperone / positive regulation of endothelial cell migration / protein export from nucleus / acrosomal vesicle / protein maturation / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to virus / intracellular calcium ion homeostasis / phagocytic vesicle membrane / cellular senescence / integrin binding / unfolded protein binding / nuclear envelope / protein folding / response to estradiol / protein-folding chaperone binding / ER-Phagosome pathway / carbohydrate binding / spermatogenesis / regulation of apoptotic process / postsynapse / negative regulation of translation / protein stabilization / ribosome / iron ion binding / response to xenobiotic stimulus / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / positive regulation of cell population proliferation / calcium ion binding / ubiquitin protein ligase binding / positive regulation of gene expression / endoplasmic reticulum membrane / regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Jelly Rolls - #200 ...Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsGaboriaud, 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.
#1: Journal: PLoS ONE / Year: 2011
Title: X-ray structure of the human calreticulin globular domain reveals a peptide-binding area and suggests a multi-molecular mechanism.
Authors: Chouquet, A. / Paidassi, H. / Ling, W.L. / Frachet, P. / Houen, G. / Arlaud, G.J. / Gaboriaud, C.
History
DepositionJul 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Aug 1, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_related_exp_data_set
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)302,04021
Polymers301,60410
Non-polymers43611
Water17,312961
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-98 kcal/mol
Surface area104410 Å2
MethodPISA
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 number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA18 - 3679 - 264
21GLUGLULEULEUBB18 - 3679 - 264
12PROPROARGARGAA19 - 36610 - 263
22PROPROARGARGCC19 - 36610 - 263
13GLUGLULEULEUAA18 - 3679 - 264
23GLUGLULEULEUDD18 - 3679 - 264
14PROPROARGARGAA19 - 36610 - 263
24PROPROARGARGEE19 - 36610 - 263
15PROPROARGARGAA19 - 36610 - 263
25PROPROARGARGFF19 - 36610 - 263
16PROPROARGARGAA19 - 36610 - 263
26PROPROARGARGGG19 - 36610 - 263
17PROPROGLNGLNAA19 - 36510 - 262
27PROPROGLNGLNHH19 - 36510 - 262
18PROPROLEULEUAA19 - 36710 - 264
28PROPROLEULEUII19 - 36710 - 264
19PROPROARGARGAA19 - 36610 - 263
29PROPROARGARGJJ19 - 36610 - 263
110PROPROLEULEUBB19 - 36710 - 264
210PROPROLEULEUCC19 - 36710 - 264
111GLUGLULEULEUBB18 - 3679 - 264
211GLUGLULEULEUDD18 - 3679 - 264
112PROPROGLNGLNBB19 - 36510 - 262
212PROPROGLNGLNEE19 - 36510 - 262
113PROPROLEULEUBB19 - 36710 - 264
213PROPROLEULEUFF19 - 36710 - 264
114PROPROLEULEUBB19 - 36710 - 264
214PROPROLEULEUGG19 - 36710 - 264
115PROPROARGARGBB19 - 36610 - 263
215PROPROARGARGHH19 - 36610 - 263
116PROPROARGARGBB19 - 36610 - 263
216PROPROARGARGII19 - 36610 - 263
117PROPROLEULEUBB19 - 36710 - 264
217PROPROLEULEUJJ19 - 36710 - 264
118PROPROARGARGCC19 - 36610 - 263
218PROPROARGARGDD19 - 36610 - 263
119PROPROARGARGCC19 - 36610 - 263
219PROPROARGARGEE19 - 36610 - 263
120PROPROLEULEUCC19 - 36710 - 264
220PROPROLEULEUFF19 - 36710 - 264
121PROPROLEULEUCC19 - 36710 - 264
221PROPROLEULEUGG19 - 36710 - 264
122PROPROGLNGLNCC19 - 36510 - 262
222PROPROGLNGLNHH19 - 36510 - 262
123PROPROLEULEUCC19 - 36710 - 264
223PROPROLEULEUII19 - 36710 - 264
124PROPROLEULEUCC19 - 36710 - 264
224PROPROLEULEUJJ19 - 36710 - 264
125PROPROARGARGDD19 - 36610 - 263
225PROPROARGARGEE19 - 36610 - 263
126PROPROARGARGDD19 - 36610 - 263
226PROPROARGARGFF19 - 36610 - 263
127PROPROARGARGDD19 - 36610 - 263
227PROPROARGARGGG19 - 36610 - 263
128PROPROGLNGLNDD19 - 36510 - 262
228PROPROGLNGLNHH19 - 36510 - 262
129PROPROLEULEUDD19 - 36710 - 264
229PROPROLEULEUII19 - 36710 - 264
130PROPROARGARGDD19 - 36610 - 263
230PROPROARGARGJJ19 - 36610 - 263
131PROPROARGARGEE19 - 36610 - 263
231PROPROARGARGFF19 - 36610 - 263
132PROPROARGARGEE19 - 36610 - 263
232PROPROARGARGGG19 - 36610 - 263
133PROPROARGARGEE19 - 36610 - 263
233PROPROARGARGHH19 - 36610 - 263
134PROPROGLNGLNEE19 - 36510 - 262
234PROPROGLNGLNII19 - 36510 - 262
135PROPROARGARGEE19 - 36610 - 263
235PROPROARGARGJJ19 - 36610 - 263
136PROPROLEULEUFF19 - 36710 - 264
236PROPROLEULEUGG19 - 36710 - 264
137PROPROGLNGLNFF19 - 36510 - 262
237PROPROGLNGLNHH19 - 36510 - 262
138PROPROLEULEUFF19 - 36710 - 264
238PROPROLEULEUII19 - 36710 - 264
139PROPROLEULEUFF19 - 36710 - 264
239PROPROLEULEUJJ19 - 36710 - 264
140PROPROGLNGLNGG19 - 36510 - 262
240PROPROGLNGLNHH19 - 36510 - 262
141PROPROLEULEUGG19 - 36710 - 264
241PROPROLEULEUII19 - 36710 - 264
142PROPROLEULEUGG19 - 36710 - 264
242PROPROLEULEUJJ19 - 36710 - 264
143PROPROARGARGHH19 - 36610 - 263
243PROPROARGARGII19 - 36610 - 263
144PROPROGLNGLNHH19 - 36510 - 262
244PROPROGLNGLNJJ19 - 36510 - 262
145PROPROLEULEUII19 - 36710 - 264
245PROPROLEULEUJJ19 - 36710 - 264

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#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 (CDC Enteric Group 11)
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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 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
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.3→47.77 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.24685 5630 5 %RANDOM
Rwork0.21027 ---
obs0.21211 107101 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.726 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20353 0 11 961 21325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01920931
X-RAY DIFFRACTIONr_bond_other_d0.010.0218756
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.93428172
X-RAY DIFFRACTIONr_angle_other_deg1.6643.00143388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78852520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55325.7091114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.779153525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.781544
X-RAY DIFFRACTIONr_chiral_restr0.0940.22882
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0224080
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024968
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8412.2210161
X-RAY DIFFRACTIONr_mcbond_other1.842.21910160
X-RAY DIFFRACTIONr_mcangle_it2.8413.31912631
X-RAY DIFFRACTIONr_mcangle_other2.8413.3212632
X-RAY DIFFRACTIONr_scbond_it2.7132.47210770
X-RAY DIFFRACTIONr_scbond_other2.7132.47210771
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3033.59815541
X-RAY DIFFRACTIONr_long_range_B_refined5.96418.0223971
X-RAY DIFFRACTIONr_long_range_B_other5.93317.99523742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A153290.07
12B153290.07
21A144850.11
22C144850.11
31A150360.1
32D150360.1
41A143980.12
42E143980.12
51A147370.1
52F147370.1
61A148280.11
62G148280.11
71A146500.11
72H146500.11
81A145050.12
82I145050.12
91A145000.12
92J145000.12
101B144140.11
102C144140.11
111B147670.1
112D147670.1
121B144820.12
122E144820.12
131B147290.1
132F147290.1
141B147760.1
142G147760.1
151B145450.11
152H145450.11
161B144870.11
162I144870.11
171B144880.12
172J144880.12
181C145810.11
182D145810.11
191C145500.11
192E145500.11
201C148160.1
202F148160.1
211C149530.1
212G149530.1
221C145580.11
222H145580.11
231C144750.11
232I144750.11
241C148250.1
242J148250.1
251D145690.11
252E145690.11
261D148670.1
262F148670.1
271D147530.1
272G147530.1
281D146370.1
282H146370.1
291D145240.11
292I145240.11
301D146670.11
302J146670.11
311E145320.11
312F145320.11
321E145580.12
322G145580.12
331E143610.12
332H143610.12
341E145890.12
342I145890.12
351E145920.12
352J145920.12
361F149500.1
362G149500.1
371F145830.11
372H145830.11
381F144690.11
382I144690.11
391F148380.1
392J148380.1
401G147330.11
402H147330.11
411G144920.11
412I144920.11
421G149700.1
422J149700.1
431H144230.12
432I144230.12
441H147730.11
442J147730.11
451I145570.11
452J145570.11
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 377 -
Rwork0.27 6540 -
obs--81.54 %

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