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- PDB-3ici: Crystal structure of cyclophilin B in complex with calmegin fragment -

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Basic information

Entry
Database: PDB / ID: 3ici
TitleCrystal structure of cyclophilin B in complex with calmegin fragment
Components
  • Calnexin
  • Peptidyl-prolyl cis-trans isomerase B
KeywordsISOMERASE / protein-protein complex / Endoplasmic reticulum / Glycoprotein / Rotamase / Chaperone / Lectin / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


endoplasmic reticulum chaperone complex / host-mediated activation of viral genome replication / Collagen biosynthesis and modifying enzymes / host-mediated activation of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / : / ERAD pathway ...endoplasmic reticulum chaperone complex / host-mediated activation of viral genome replication / Collagen biosynthesis and modifying enzymes / host-mediated activation of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / : / ERAD pathway / neutrophil chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / bone development / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / melanosome / protein folding / protein stabilization / endoplasmic reticulum lumen / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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. / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site ...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. / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Calmegin / Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesHomo sapiens (human)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Basis of Cyclophilin B Binding by the Calnexin/Calreticulin P-domain.
Authors: Kozlov, G. / Bastos-Aristizabal, S. / Maattanen, P. / Rosenauer, A. / Zheng, F. / Killikelly, A. / Trempe, J.F. / Thomas, D.Y. / Gehring, K.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _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_ref_seq_dif.details / _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: Peptidyl-prolyl cis-trans isomerase B
B: Peptidyl-prolyl cis-trans isomerase B
C: Calnexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1406
Polymers45,8143
Non-polymers3263
Water9,080504
1
A: Peptidyl-prolyl cis-trans isomerase B
C: Calnexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3394
Polymers25,0782
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-3.4 kcal/mol
Surface area9310 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8012
Polymers20,7361
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.411, 44.295, 55.427
Angle α, β, γ (deg.)89.94, 94.46, 114.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase B / PPIase / Rotamase / Cyclophilin B / S-cyclophilin / SCYLP / CYP-S1


Mass: 20735.787 Da / Num. of mol.: 2 / Fragment: UNP residues 34-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIB, CYPB / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23284, peptidylprolyl isomerase
#2: Protein/peptide Calnexin / pp90


Mass: 4342.601 Da / Num. of mol.: 1 / Fragment: P-domain fragment: residues 317-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: CANX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: PDB-D9N169, UniProt: E2RA18*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE SEQUENCE OF ENTITY 2 (CHAIN C) CORRESPONDS TO RESIDUES 317-350 OF DOG ...AUTHORS STATE THAT THE SEQUENCE OF ENTITY 2 (CHAIN C) CORRESPONDS TO RESIDUES 317-350 OF DOG CALMEGIN, NCBI REFERENCE SEQUENCE XP_533285.

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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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% w/v PEG 8000, 10mM ZnCl2, 0.1M Tris buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9995 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2008 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9995 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 38845 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2598 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CYN

1cyn


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.316 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23876 1998 5 %RANDOM
Rwork0.18773 ---
all0.19037 37796 --
obs0.19037 37796 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.291 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å21.09 Å20.24 Å2
2--0.2 Å20.36 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 14 504 3487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223100
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9644171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7924.318132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83315570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5461514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022316
X-RAY DIFFRACTIONr_nbd_refined0.2090.21476
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2365
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.238
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0170.22
X-RAY DIFFRACTIONr_mcbond_it0.8651.51932
X-RAY DIFFRACTIONr_mcangle_it1.43623062
X-RAY DIFFRACTIONr_scbond_it2.37831291
X-RAY DIFFRACTIONr_scangle_it3.8544.51099
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 164 -
Rwork0.223 2598 -
obs--91.43 %

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