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- PDB-1cnt: CILIARY NEUROTROPHIC FACTOR -

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Basic information

Entry
Database: PDB / ID: 1cnt
TitleCILIARY NEUROTROPHIC FACTOR
ComponentsCILIARY NEUROTROPHIC FACTOR
KeywordsCYTOKINE / NEUROTROPHIC FACTOR / GROWTH FACTOR
Function / homology
Function and homology information


retinal rod cell differentiation / regulation of retinal cell programmed cell death / muscle organ morphogenesis / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / negative regulation of photoreceptor cell differentiation / interleukin-6 receptor binding / IL-6-type cytokine receptor ligand interactions / positive regulation of axon regeneration / neuron development ...retinal rod cell differentiation / regulation of retinal cell programmed cell death / muscle organ morphogenesis / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / negative regulation of photoreceptor cell differentiation / interleukin-6 receptor binding / IL-6-type cytokine receptor ligand interactions / positive regulation of axon regeneration / neuron development / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / astrocyte activation / growth factor activity / negative regulation of neuron apoptotic process / axon / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Ciliary neurotrophic factor, CNTF / Ciliary neurotrophic factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
YTTERBIUM (III) ION / Ciliary neurotrophic factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMcdonald, N.Q. / Panayotatos, N. / Hendrickson, W.A.
CitationJournal: EMBO J. / Year: 1995
Title: Crystal structure of dimeric human ciliary neurotrophic factor determined by MAD phasing.
Authors: McDonald, N.Q. / Panayotatos, N. / Hendrickson, W.A.
History
DepositionJun 6, 1996Processing site: BNL
Revision 1.0Mar 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
1: CILIARY NEUROTROPHIC FACTOR
2: CILIARY NEUROTROPHIC FACTOR
3: CILIARY NEUROTROPHIC FACTOR
4: CILIARY NEUROTROPHIC FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5039
Polymers85,9464
Non-polymers5575
Water2,684149
1
1: CILIARY NEUROTROPHIC FACTOR
4: CILIARY NEUROTROPHIC FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1654
Polymers42,9732
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2: CILIARY NEUROTROPHIC FACTOR
3: CILIARY NEUROTROPHIC FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3385
Polymers42,9732
Non-polymers3653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.950, 62.090, 208.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.98461, 0.16803, -0.04808), (0.1716, 0.87722, -0.44838), (-0.03316, -0.44973, -0.89255)96.77232, 17.47824, 108.88966
2given(-0.76828, 0.63677, 0.06535), (0.63991, 0.76144, 0.10355), (0.01618, 0.12138, -0.99247)40.33489, -28.7394, 216.09

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Components

#1: Protein
CILIARY NEUROTROPHIC FACTOR / CNTF


Mass: 21486.400 Da / Num. of mol.: 4 / Mutation: 13 C-TERMINAL RESIDUES DELETED IN THIS CONSTRUCT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN CNTF / Plasmid: CLASSIFIED / Gene (production host): HUMAN CNTF / Production host: Escherichia coli (E. coli) / References: UniProt: P26441
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.41 % / Description: MAD EXPERIMENT AT LIII EDGE OF YTTERBIUM
Crystal grow
*PLUS
pH: 6.35 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
23.75 %PEG80001drop
30.075 Mammonium sulfate1drop
41 mMdithiothreitol1drop
525 mMsodium citrate1drop
67.5 %PEG80001reservoir
70.15 Mammonium sulfate1reservoir
82 mMdithiothreitol1reservoir
950 mMsodium citrate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.37 / Wavelength: 1.37, 1.39
DetectorDetector: IMAGE PLATE / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.371
21.391
ReflectionResolution: 2.4→20 Å / Redundancy: 4 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Num. obs: 18227 / % possible obs: 92.8 % / Num. measured all: 40431

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.4→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.247 -
Rwork0.199 -
obs0.199 41229
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 21 149 4926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.087
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it21
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it3.351.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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