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- PDB-3u83: Crystal structure of nectin-1 -

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Basic information

Entry
Database: PDB / ID: 3u83
TitleCrystal structure of nectin-1
ComponentsPoliovirus receptor-related protein 1
KeywordsCELL ADHESION / nectin-1 / hinge region plasiticity
Function / homology
Function and homology information


desmosome organization / Nectin/Necl trans heterodimerization / cell adhesion mediator activity / cochlea morphogenesis / protein localization to cell junction / lens morphogenesis in camera-type eye / enamel mineralization / growth cone membrane / cell-cell contact zone / virion binding ...desmosome organization / Nectin/Necl trans heterodimerization / cell adhesion mediator activity / cochlea morphogenesis / protein localization to cell junction / lens morphogenesis in camera-type eye / enamel mineralization / growth cone membrane / cell-cell contact zone / virion binding / Adherens junctions interactions / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / apical junction complex / regulation of synapse assembly / homophilic cell adhesion via plasma membrane adhesion molecules / coreceptor activity / cell adhesion molecule binding / presynaptic active zone membrane / axon guidance / hippocampal mossy fiber to CA3 synapse / adherens junction / cell-cell adhesion / iron ion transport / virus receptor activity / retina development in camera-type eye / carbohydrate binding / cell adhesion / immune response / symbiont entry into host cell / dendrite / protein-containing complex binding / protein homodimerization activity / extracellular region / identical protein binding / membrane / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsZhang, N. / Yan, J. / Lu, G. / Guo, Z. / Fan, Z. / Wang, J. / Shi, Y. / Qi, J. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2011
Title: Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell adhesion.
Authors: Zhang, N. / Yan, J. / Lu, G. / Guo, Z. / Fan, Z. / Wang, J. / Shi, Y. / Qi, J. / Gao, G.F.
History
DepositionOct 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,2052
Polymers36,9381
Non-polymers2661
Water3,207178
1
A: Poliovirus receptor-related protein 1
hetero molecules

A: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4104
Polymers73,8772
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area2100 Å2
ΔGint-3 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.520, 127.520, 190.555
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 36938.492 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 30-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVRL1, HVEC, PRR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15223
#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.04 Å3/Da / Density % sol: 69.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 2000, 0.2M Trimethylamine N-oxidedihydrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 20827 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 20.933
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 4.739 / Num. unique all: 2037 / Rsym value: 0.594 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ALP

3alp


Resolution: 2.499→40.774 Å / SU ML: 0.28 / σ(F): 0.18 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 1023 5.11 %RANDOM
Rwork0.185 ---
all0.1873 ---
obs0.1873 20026 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.468 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0772 Å2-0 Å2-0 Å2
2--4.0772 Å20 Å2
3----8.1544 Å2
Refinement stepCycle: LAST / Resolution: 2.499→40.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 16 178 2544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052432
X-RAY DIFFRACTIONf_angle_d1.0033304
X-RAY DIFFRACTIONf_dihedral_angle_d19.579887
X-RAY DIFFRACTIONf_chiral_restr0.065369
X-RAY DIFFRACTIONf_plane_restr0.003431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4989-2.63070.30961460.2385244988
2.6307-2.79550.26131340.2179257893
2.7955-3.01120.25891420.204269896
3.0112-3.31410.24841580.1976271197
3.3141-3.79340.25521640.1788279999
3.7934-4.77810.18441450.1559283099
4.7781-40.77940.17971340.164293899
Refinement TLS params.Method: refined / Origin x: -16.7312 Å / Origin y: -5.0264 Å / Origin z: -33.4212 Å
111213212223313233
T0.1732 Å20.0091 Å2-0.0097 Å2-0.168 Å20.008 Å2--0.1613 Å2
L0.7305 °2-0.5312 °20.6813 °2-0.3987 °2-0.4776 °2--0.5724 °2
S-0.0348 Å °-0.0218 Å °-0.0121 Å °-0.0284 Å °0.0288 Å °0.0111 Å °-0.0186 Å °-0.0045 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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