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- PDB-3alp: Cell adhesion protein -

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Basic information

Entry
Database: PDB / ID: 3alp
TitleCell adhesion protein
ComponentsPoliovirus receptor-related protein 1
KeywordsCELL ADHESION / immunoglobulin-like domain / V-set / C2-set
Function / homology
Function and homology information


desmosome organization / Nectin/Necl trans heterodimerization / protein localization to cell junction / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / cell-cell contact zone / Adherens junctions interactions / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...desmosome organization / Nectin/Necl trans heterodimerization / protein localization to cell junction / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / cell-cell contact zone / Adherens junctions interactions / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / apical junction complex / homophilic cell adhesion via plasma membrane adhesion molecules / coreceptor activity / presynaptic active zone membrane / hippocampal mossy fiber to CA3 synapse / cell adhesion molecule binding / axon guidance / adherens junction / cell-cell adhesion / virus receptor activity / retina development in camera-type eye / iron ion transport / carbohydrate binding / cell adhesion / immune response / symbiont entry into host cell / dendrite / protein-containing complex binding / protein homodimerization activity / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
CITRIC ACID / HEXANE-1,6-DIOL / Nectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsNarita, H. / Nakagawa, A. / Suzuki, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of the cis-Dimer of Nectin-1: implications for the architecture of cell-cell junctions
Authors: Narita, H. / Yamamoto, Y. / Suzuki, M. / Miyazaki, N. / Yoshida, A. / Kawai, K. / Iwasaki, K. / Nakagawa, A. / Takai, Y. / Sakisaka, T.
History
DepositionAug 5, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poliovirus receptor-related protein 1
B: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3795
Polymers73,8772
Non-polymers5023
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-7 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.924, 164.924, 164.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Poliovirus receptor-related protein 1 / Herpes virus entry mediator C / Herpesvirus entry mediator C / HveC / Nectin-1 / Herpesvirus Ig- ...Herpes virus entry mediator C / Herpesvirus entry mediator C / HveC / Nectin-1 / Herpesvirus Ig-like receptor / HIgR


Mass: 36938.492 Da / Num. of mol.: 2 / Fragment: extracellular region (UNP RESIDUES 30-335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVEC, PRR1, PVRL1 / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15223
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 5.06 Å3/Da / Density % sol: 75.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1% PEG 3350, 50mM Bis-Tris propane, 50mM citric acid, 6% hexane-1,6-diol , VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU21.07195
Detector
TypeIDDetectorDateDetails
Bruker DIP-60401CCDMar 9, 2009mirror
Bruker DIP-60402CCDFeb 10, 2009mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.071951
ReflectionResolution: 2.8→50 Å / Num. obs: 36109 / % possible obs: 97.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 4.3 / Num. unique all: 13666 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.804→35.989 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1747 5.03 %RANDAM
Rwork0.1899 ---
obs0.1917 34698 94.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.604 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 80.04 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.804→35.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 34 37 4717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014797
X-RAY DIFFRACTIONf_angle_d1.2476544
X-RAY DIFFRACTIONf_dihedral_angle_d17.461725
X-RAY DIFFRACTIONf_chiral_restr0.077741
X-RAY DIFFRACTIONf_plane_restr0.008861
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8038-2.88630.32971080.2546245084
2.8863-2.97940.30261260.2498249187
2.9794-3.08580.28481340.2453255989
3.0858-3.20930.28471490.2352265592
3.2093-3.35520.29031600.2184267394
3.3552-3.5320.2741320.205278096
3.532-3.75310.23051480.194280397
3.7531-4.04250.23531590.1817284597
4.0425-4.44860.18761650.1471286299
4.4486-5.09080.20381450.1375291499
5.0908-6.4080.19141530.17332949100
6.408-35.99230.18981680.1952297097
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)
10.48910.87430.58411.34870.72151.6688-0.0480.23010.15-0.06380.3029-0.2606-0.06830.3414-0.19210.2735-0.00490.09430.47090.09040.410142.593236.89014.5368
20.47350.4148-0.18880.17270.95561.6708-0.0345-0.09060.25820.1328-0.01330.18450.2580.15260.02660.31040.050.16570.21470.05840.316426.623149.119537.8937
3-0.0753-0.14350.40742.48852.67653.7484-0.4288-0.04460.09180.6769-0.52580.88060.2527-0.10810.7020.932-0.09120.34970.5042-0.30640.797823.184771.035774.1203
42.22061.40450.49842.05820.88850.5926-0.23420.2331-0.0106-0.24030.2404-0.03790.09380.1680.02190.31860.02280.10630.36740.09950.225132.804717.8231-7.1463
51.01561.8443-0.77732.5132-1.34541.60170.0260.0120.068-0.1303-0.0259-0.0370.2241-0.2054-0.00260.27520.01830.10910.32790.1340.307511.2403-8.471111.009
62.38272.5516-1.40512.1506-1.43430.5188-0.59520.6533-0.3447-0.67860.2786-0.42080.3317-0.42530.26220.7167-0.28570.23580.5674-0.09250.4556-12.5245-44.200915.9795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 21:130)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 131:231)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 232:321)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 18:130)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 131:231)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 232:321)

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