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- PDB-1jhn: Crystal Structure of the Lumenal Domain of Calnexin -

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Basic information

Entry
Database: PDB / ID: 1jhn
TitleCrystal Structure of the Lumenal Domain of Calnexin
Componentscalnexin
KeywordsCHAPERONE / jelly-roll / beta sandwich
Function / homology
Function and homology information


melanosome membrane / clathrin-dependent endocytosis / synaptic vesicle endocytosis / ERAD pathway / mitochondrial membrane / unfolded protein binding / protein folding / presynapse / carbohydrate binding / calcium ion binding ...melanosome membrane / clathrin-dependent endocytosis / synaptic vesicle endocytosis / ERAD pathway / mitochondrial membrane / unfolded protein binding / protein folding / presynapse / carbohydrate binding / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Calnexin lumenal domain, non-globular proline-rich hairpin domain / Calreticulin/calnexin, P domain / 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. / Jelly Rolls - #200 ...Calnexin lumenal domain, non-globular proline-rich hairpin domain / Calreticulin/calnexin, P domain / 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. / Jelly Rolls - #200 / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS, SAS, MAD / Resolution: 2.9 Å
AuthorsSchrag, J.D. / Bergeron, J.M. / Li, Y. / Borisova, S. / Hahn, M. / Thomas, D.Y. / Cygler, M.
Citation
Journal: Mol.Cell / Year: 2001
Title: The Structure of calnexin, an ER chaperone involved in quality control of protein folding.
Authors: Schrag, J.D. / Bergeron, J.J. / Li, Y. / Borisova, S. / Hahn, M. / Thomas, D.Y. / Cygler, M.
#1: Journal: J.Struct.Biol. / Year: 1998
Title: Identification and Crystallization of a Protease-Resistant Core of Calnexin that Retains Biological Activity
Authors: Hahn, M. / Borisova, S. / Schrag, J.D. / Tessier, D.C. / Zapun, A. / Tom, R. / Kamen, A.A. / Bergeron, J.J. / Thomas, D.Y. / Cygler, M.
History
DepositionJun 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_sheet / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: calnexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3322
Polymers48,2921
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.772, 85.772, 143.476
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein calnexin


Mass: 48291.766 Da / Num. of mol.: 1 / Fragment: lumenal domain (residues 45-468)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Cell line: SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24643
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, MPD, Calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: used microseeding, Hahn, M., (1998) J. Struct. Biol., 123, 260.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 %MPD1drop
320 mMHEPES1drop
41 mM1dropCaCl2
52 %sucrose1drop
625 %MPD1reservoir
710 %PEG80001reservoir
8150 mMHEPES1reservoir
95 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.4 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 1999
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. all: 12339 / Num. obs: 12339 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 84.5 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 23.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.245 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 82347
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MIRAS, SAS, MAD / Resolution: 2.9→33.8 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh and Huber / Details: phase restraints used
RfactorNum. reflectionSelection details
Rfree0.377 529 random
Rwork0.327 --
all-12318 -
obs-11392 -
Displacement parametersBiso mean: 59.5 Å2
Baniso -1Baniso -2Baniso -3
1--11.9 Å20 Å20 Å2
2---11.9 Å20 Å2
3---23.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.76 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a1.06 Å0.82 Å
Refinement stepCycle: LAST / Resolution: 2.9→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 1 0 2854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.41
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 33.8 Å / σ(F): 4 / Rfactor obs: 0.327
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41

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