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- PDB-1qz1: Crystal Structure of the Ig 1-2-3 fragment of NCAM -

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Basic information

Entry
Database: PDB / ID: 1qz1
TitleCrystal Structure of the Ig 1-2-3 fragment of NCAM
ComponentsNeural cell adhesion molecule 1, 140 kDa isoform
KeywordsCELL ADHESION / IG MODULES / NCAM
Function / homology
Function and homology information


NCAM1 interactions / regulation of exocyst assembly / regulation of semaphorin-plexin signaling pathway / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / cellular response to molecule of bacterial origin / peripheral nervous system axon regeneration / LRR domain binding / homotypic cell-cell adhesion / NCAM signaling for neurite out-growth / Signal transduction by L1 ...NCAM1 interactions / regulation of exocyst assembly / regulation of semaphorin-plexin signaling pathway / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / cellular response to molecule of bacterial origin / peripheral nervous system axon regeneration / LRR domain binding / homotypic cell-cell adhesion / NCAM signaling for neurite out-growth / Signal transduction by L1 / cellular response to inorganic substance / thalamus development / fibroblast growth factor receptor binding / commissural neuron axon guidance / axonal fasciculation / negative regulation of programmed cell death / RAF/MAP kinase cascade / response to inorganic substance / neuron development / epithelial to mesenchymal transition / multicellular organismal response to stress / phosphatase binding / animal organ regeneration / positive regulation of calcium-mediated signaling / positive regulation of cardiac muscle cell proliferation / cytoskeletal protein binding / response to activity / response to cocaine / calcium-mediated signaling / response to lead ion / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron projection development / cell-cell junction / presynaptic membrane / heparin binding / growth cone / postsynaptic membrane / learning or memory / cell surface receptor signaling pathway / cell adhesion / response to xenobiotic stimulus / axon / external side of plasma membrane / neuronal cell body / glutamatergic synapse / cell surface / plasma membrane
Similarity search - Function
Neural cell adhesion / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III ...Neural cell adhesion / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSoroka, V. / Kolkova, K. / Kastrup, J.S. / Diederichs, K. / Breed, J. / Kiselyov, V.V. / Poulsen, F.M. / Larsen, I.K. / Welte, W. / Berezin, V. ...Soroka, V. / Kolkova, K. / Kastrup, J.S. / Diederichs, K. / Breed, J. / Kiselyov, V.V. / Poulsen, F.M. / Larsen, I.K. / Welte, W. / Berezin, V. / Bock, E. / Kasper, C.
Citation
Journal: Structure / Year: 2003
Title: Structure and interactions of NCAM Ig1-2-3 suggest a novel zipper mechanism for homophilic adhesion
Authors: Soroka, V. / Kolkova, K. / Kastrup, J.S. / Diederichs, K. / Breed, J. / Kiselyov, V.V. / Poulsen, F.M. / Larsen, I.K. / Welte, W. / Berezin, V. / Bock, E. / Kasper, C.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: STRUCTURAL BASIS OF CELL-CELL ADHESION BY NCAM
Authors: Kasper, C. / Rasmussen, H. / Kastrup, J.S. / Ikemizu, S. / Jones, E.Y. / Berezin, V. / Bock, E. / Larsen, I.K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression, crystallization and preliminary X-ray analysis of the two amino-terminal Ig domains of the neural cell adhesion molecule (NCAM)
Authors: Kasper, C. / Rasmussen, H. / Berezin, V. / Bock, E. / Larsen, I.K.
History
DepositionSep 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE Residues -2, 239 and 240 were not visible in the electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neural cell adhesion molecule 1, 140 kDa isoform


Theoretical massNumber of molelcules
Total (without water)32,4071
Polymers32,4071
Non-polymers00
Water4,774265
1
A: Neural cell adhesion molecule 1, 140 kDa isoform

A: Neural cell adhesion molecule 1, 140 kDa isoform


Theoretical massNumber of molelcules
Total (without water)64,8142
Polymers64,8142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Unit cell
Length a, b, c (Å)51.440, 107.760, 149.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe biological assembly is a dimer. The second part of the biological assembly is generated by the rotation (-x, y, -z) and the translation (0.5, 0, 0)

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Components

#1: Protein Neural cell adhesion molecule 1, 140 kDa isoform / / N-CAM 140 / NCAM-140


Mass: 32407.225 Da / Num. of mol.: 1 / Fragment: IG MODULES 1-2-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NCAM1 / Plasmid: pHIL-S1 / Production host: Pichia pastoris (fungus) / Strain (production host): GS-115 / References: UniProt: P13596
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 14-17% PEG 4000, 450 mM Li sulfate, 100 mM Na acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
25 mMsodium phosphate1drop
3150 mM1droppH7.4NaCl
414-17 %(w/v)PEG40001reservoir
5450 mMlithium sulfate1reservoir
6100 mMsodium acetate1reservoirpH5.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONMAX II I71111.0526
ROTATING ANODEOTHER21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATENov 6, 2000
MARRESEARCH2IMAGE PLATEDec 4, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.05261
21.54181
ReflectionResolution: 2→50 Å / Num. all: 27881 / Num. obs: 27881 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2756 / Rsym value: 0.209 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 164206
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EPF

1epf


Resolution: 2→48.64 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 241-242 were not located in the electron density map
RfactorNum. reflection% reflectionSelection details
Rfree0.238 828 -RANDOM
Rwork0.218 ---
all-28289 --
obs-28289 99.2 %-
Displacement parametersBiso mean: 60.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.9 Å20 Å20 Å2
2---15.2 Å20 Å2
3---7.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 0 265 2512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.036
RfactorNum. reflection% reflection
Rfree0.439 148 -
Rwork0.373 --
obs-4474 99 %
Refinement
*PLUS
% reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0081
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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