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- PDB-2vkx: Human NCAM, FN3 domains 1 and 2, M610R mutant -

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Basic information

Entry
Database: PDB / ID: 2vkx
TitleHuman NCAM, FN3 domains 1 and 2, M610R mutant
ComponentsNEURAL CELL ADHESION MOLECULE
KeywordsCELL ADHESION / ADHESION RECEPTOR
Function / homology
Function and homology information


regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / epithelial to mesenchymal transition / ECM proteoglycans / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / : / virus receptor activity ...regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / epithelial to mesenchymal transition / ECM proteoglycans / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / : / virus receptor activity / RAF/MAP kinase cascade / cell adhesion / neuron projection / Golgi membrane / external side of plasma membrane / cell surface / extracellular region / membrane / plasma membrane / cytosol
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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCarafoli, F. / Saffell, J.L. / Hohenester, E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the Tandem Fibronectin Type 3 Domains of Neural Cell Adhesion Molecule
Authors: Carafoli, F. / Saffell, J.L. / Hohenester, E.
History
DepositionJan 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEURAL CELL ADHESION MOLECULE
B: NEURAL CELL ADHESION MOLECULE
C: NEURAL CELL ADHESION MOLECULE
D: NEURAL CELL ADHESION MOLECULE
E: NEURAL CELL ADHESION MOLECULE
F: NEURAL CELL ADHESION MOLECULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,82317
Polymers138,7676
Non-polymers1,05711
Water55831
1
A: NEURAL CELL ADHESION MOLECULE
B: NEURAL CELL ADHESION MOLECULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4484
Polymers46,2562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-9.9 kcal/mol
Surface area23640 Å2
MethodPQS
2
C: NEURAL CELL ADHESION MOLECULE
D: NEURAL CELL ADHESION MOLECULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5445
Polymers46,2562
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-16.7 kcal/mol
Surface area23490 Å2
MethodPQS
3
E: NEURAL CELL ADHESION MOLECULE
F: NEURAL CELL ADHESION MOLECULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8328
Polymers46,2562
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-8.5 kcal/mol
Surface area23940 Å2
MethodPQS
Unit cell
Length a, b, c (Å)92.419, 107.573, 161.124
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(-0.54446, 0.54095, -0.64104), (0.54423, -0.35371, -0.76072), (-0.63826, -0.76306, -0.10182)35.9921, 86.42128, 98.64619
2given(0.20885, 0.81779, 0.53629), (-0.38988, -0.43329, 0.81256), (0.89687, -0.37879, 0.22835)-50.07765, 22.99, 40.46176
3given(-0.03922, -0.57884, -0.81449), (-0.55368, -0.66596, 0.49994), (-0.83181, 0.47058, -0.29437)81.79694, 51.2503, 60.17155
4given(0.21969, -0.47301, 0.85323), (0.76445, -0.4599, -0.45179), (0.6061, 0.7515, 0.26055)-12.58587, 70.74368, -2.45363
5given(-0.92515, -0.36364, 0.10891), (-0.37226, 0.92527, -0.07282), (-0.07429, -0.10791, -0.99138)39.7716, 12.85621, 108.87283

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Components

#1: Protein
NEURAL CELL ADHESION MOLECULE / N-CAM 140 / NCAM-140 / CD56 ANTIGEN


Mass: 23127.775 Da / Num. of mol.: 6 / Fragment: FN3 DOMAINS, RESIDUES 496-598,601-692 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P13591
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 611 TO ARG ENGINEERED RESIDUE IN CHAIN B, MET 611 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, MET 611 TO ARG ENGINEERED RESIDUE IN CHAIN B, MET 611 TO ARG ENGINEERED RESIDUE IN CHAIN C, MET 611 TO ARG ENGINEERED RESIDUE IN CHAIN D, MET 611 TO ARG ENGINEERED RESIDUE IN CHAIN E, MET 611 TO ARG ENGINEERED RESIDUE IN CHAIN F, MET 611 TO ARG
Sequence detailsN-TERMINAL APLA AND C-TERMINAL AAAHHHHHH ARE VECTOR- DERIVED. QG (POSITIONS 599-600) OF P13591 ...N-TERMINAL APLA AND C-TERMINAL AAAHHHHHH ARE VECTOR- DERIVED. QG (POSITIONS 599-600) OF P13591 REPLACED BY R ( NATURAL MUSCLE- AND BRAIN-SPECIFIC SPLICE VARIANT). M610 REPLACED BY R (DESIGNED MUTATION).

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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: 3.06 Å3/Da / Density % sol: 59.48 % / Description: NONE
Crystal growpH: 4.6 / Details: pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.12
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 44403 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.3 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NCAM FN3 DOMAIN PAIR, WILD-TYPE

Resolution: 2.7→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 2227 5 %RANDOM
Rwork0.2233 ---
obs0.2233 44347 98.9 %-
Solvent computationBsol: 37.8006 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.854 Å20 Å20 Å2
2---7.932 Å20 Å2
3---12.785 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9264 0 55 31 9350
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.092.5

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