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- PDB-2e3v: Crystal structure of the first fibronectin type III domain of neu... -

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Basic information

Entry
Database: PDB / ID: 2e3v
TitleCrystal structure of the first fibronectin type III domain of neural cell adhesion molecule splicing isoform from human muscle culture lambda-4.4
ComponentsNeural cell adhesion molecule 1, 140 kDa isoform
KeywordsCELL ADHESION / NCAM / N-CAM 1 / NCAM-120 / CD56 antigen / membrane protein / Glycoprotein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade ...regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade / collagen-containing extracellular matrix / cell adhesion / external side of plasma membrane / Golgi 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsNishino, A. / Saijo, S. / Kishishita, S. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the first fibronectin type III domain of neural cell adhesion molecule splicing isoform from human muscle culture lambda-4.4
Authors: Saijo, S. / Nishino, A. / Kishishita, S. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S.
History
DepositionNov 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neural cell adhesion molecule 1, 140 kDa isoform
B: Neural cell adhesion molecule 1, 140 kDa isoform
C: Neural cell adhesion molecule 1, 140 kDa isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,62511
Polymers38,5263
Non-polymers1,0998
Water4,197233
1
A: Neural cell adhesion molecule 1, 140 kDa isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9482
Polymers12,8421
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neural cell adhesion molecule 1, 140 kDa isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4585
Polymers12,8421
Non-polymers6164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neural cell adhesion molecule 1, 140 kDa isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2194
Polymers12,8421
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.378, 55.378, 118.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Neural cell adhesion molecule 1, 140 kDa isoform / / N-CAM 140 / NCAM-140 / CD56 antigen / neural cell adhesion molecule / splicing isoform from human ...N-CAM 140 / NCAM-140 / CD56 antigen / neural cell adhesion molecule / splicing isoform from human muscle culture / clone lambda-4.4


Mass: 12841.971 Da / Num. of mol.: 3 / Fragment: first fibronectin type III domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAM1 / Plasmid: PK050314-05 / Production host: Cell-free protein synthesis / References: UniProt: P13591

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE RESIDUE IS ARG ACCORDING TO DICKSON G., GOWER H.J., BARTON C.H., ET AL. [CELL 50:1119-1130(1987)].

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22-25% PEG 3350, 0.1M Bis-Tris-HCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B210.979274, 0.979740, 0.964000
SYNCHROTRONAPS 22-ID20.97105
Detector
TypeIDDetectorDateDetails
RIGAKU JUPITER 2101CCDOct 3, 2006mirrors
MARMOSAIC 300 mm CCD2CCDOct 11, 2006mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiMADMx-ray1
2Si 220SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792741
20.979741
30.9641
40.971051
ReflectionResolution: 1.95→50 Å / Num. obs: 29327 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 36.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.38 / Num. unique all: 1248 / Rsym value: 0.387 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.061 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1500 5.1 %RANDOM
Rwork0.182 ---
obs0.183 27783 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 65 233 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9773252
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5685296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07425.26993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97615369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.987157
X-RAY DIFFRACTIONr_chiral_restr0.0720.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021797
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21240
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21665
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6271.51545
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79122426
X-RAY DIFFRACTIONr_scbond_it1.28331002
X-RAY DIFFRACTIONr_scangle_it1.9744.5826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 95 -
Rwork0.227 1748 -
obs-1748 83.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6181-1.3895-0.565610.07111.09333.13650.04570.14190.0590.2443-0.0192-0.19590.1999-0.1723-0.02640.0127-0.1362-0.0363-0.14490.0119-0.183828.571818.078637.8637
23.19180.6294-0.32573.6639-1.08992.87740.02680.18890.06090.0794-0.1493-0.2843-0.0394-0.01160.1225-0.015-0.1309-0.009-0.1810.0043-0.145134.17719.782436.9891
310.3328-3.47941.89946.3691-0.61765.16440.54620.714-0.3843-0.4084-0.3636-0.08010.25410.0146-0.1825-0.0231-0.15190.0321-0.22930.0417-0.20932.290518.618633.3631
455.591520.7841-42.352811.0937-23.285163.2272-0.4482-3.22340.27891.86850.0194-0.86431.3357-0.64190.42880.28780.00290.04750.5172-0.24680.472216.195136.758146.4984
510.76644.74575.85715.05543.12017.7303-0.3610.0257-0.5226-0.09570.2113-0.05570.1316-0.07420.1497-0.0054-0.1220.0911-0.1795-0.0187-0.098923.6387-0.335251.1125
62.17330.0318-0.05964.01620.49174.4289-0.1472-0.0109-0.2385-0.20110.13420.0873-0.1872-0.13110.013-0.0558-0.13840.0065-0.1677-0.0012-0.139823.784.966248.2389
76.38040.00443.84843.6765-0.562313.9734-0.0325-0.1937-0.0225-0.08890.02320.20310.2719-0.45280.0093-0.0667-0.09940.0289-0.2906-0.0091-0.105221.3194.519251.6027
87.8313.8238-4.63077.9446-3.41123.13520.1258-0.0258-0.0856-0.32850.0396-0.03390.21390.1371-0.1654-0.0561-0.1531-0.053-0.2747-0.0041-0.160121.493-21.321240.3652
96.07631.759-0.60584.5777-0.03243.76310.1952-0.47030.16430.0856-0.1187-0.10890.30320.1465-0.07650.0103-0.14660.0127-0.2017-0.0012-0.108423.2638-16.183144.7219
1011.1033-3.3214-6.72487.33572.57112.90880.1788-0.3623-0.23770.2952-0.1451-0.33170.34430.3659-0.0337-0.0391-0.2262-0.0721-0.31390.001-0.114626.2114-19.793243.8686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 266 - 24
2X-RAY DIFFRACTION2AA27 - 8825 - 86
3X-RAY DIFFRACTION3AA89 - 10787 - 105
4X-RAY DIFFRACTION4AA108 - 112106 - 110
5X-RAY DIFFRACTION5BB8 - 266 - 24
6X-RAY DIFFRACTION6BB27 - 8825 - 86
7X-RAY DIFFRACTION7BB89 - 10887 - 106
8X-RAY DIFFRACTION8CC8 - 306 - 28
9X-RAY DIFFRACTION9CC31 - 8829 - 86
10X-RAY DIFFRACTION10CC89 - 10887 - 106

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