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- PDB-4jjh: Crystal structure of the D1 domain from human Nectin-4 extracellu... -

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Basic information

Entry
Database: PDB / ID: 4jjh
TitleCrystal structure of the D1 domain from human Nectin-4 extracellular fragment [PSI-NYSGRC-005624]
ComponentsPoliovirus receptor-related protein 4
KeywordsCELL ADHESION / Nectin-4 / Ig-like D1 domain / Ig superfamily / IMMUNE SYSTEM / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / Adherens junctions interactions / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / adherens junction / virus receptor activity / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Nectin-4 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Nectin-4 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKumar, P.R. / Bonanno, J. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. ...Kumar, P.R. / Bonanno, J. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Love, J. / Patel, H. / Seidel, R. / Stead, M. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of the D1 domain of human Nectin-4 extracellular fragment [NYSGRC-005624]
Authors: Kumar, P.R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poliovirus receptor-related protein 4
B: Poliovirus receptor-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9403
Polymers28,8782
Non-polymers621
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Poliovirus receptor-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5012
Polymers14,4391
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Poliovirus receptor-related protein 4


Theoretical massNumber of molelcules
Total (without water)14,4391
Polymers14,4391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.193, 35.193, 205.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Poliovirus receptor-related protein 4 / Ig superfamily receptor LNIR / Nectin-4 / Processed poliovirus receptor-related protein 4


Mass: 14439.062 Da / Num. of mol.: 2 / Fragment: D1 domain (UNP residues 32-153)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNIR, Nectin-4, PRR4, PVRL4 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q96NY8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Chloride, 0.1M Bis-Tris:HCl, pH 6.5); Cryoprotection (Reservoir + final concentration of 20%(v/v) Ethylene ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Chloride, 0.1M Bis-Tris:HCl, pH 6.5); Cryoprotection (Reservoir + final concentration of 20%(v/v) Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.25→50 Å / Num. all: 11848 / Num. obs: 11529 / % possible obs: 97.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.069 / Χ2: 1.038 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.299.50.2625850.8421100
2.29-2.33100.2736000.8541100
2.33-2.389.90.2625940.8331100
2.38-2.42100.2415540.9051100
2.42-2.48100.2036250.9121100
2.48-2.539.90.1826000.9971100
2.53-2.69.90.1665611.0331100
2.6-2.679.90.1545811.0191100
2.67-2.759.70.136091.1331100
2.75-2.839.40.1095561.1721100
2.83-2.949.40.0986421.21100
2.94-3.059.10.0825471.205199.8
3.05-3.1990.0796171.2381100
3.19-3.368.40.0675741.231199.8
3.36-3.577.90.0615791.158196.3
3.57-3.857.80.0585601.114194.8
3.85-4.236.80.0545141.071188
4.23-4.856.40.0534711.011178.1
4.85-6.17.70.0515660.95194.3
6.1-508.30.0535940.984196.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FRW

4frw


Resolution: 2.25→35.193 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.754 / σ(F): 1.42 / Phase error: 31.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 541 4.72 %RANDOM
Rwork0.2222 ---
obs0.2257 11454 97.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.53 Å2 / Biso mean: 31.2146 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 4 1 1727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111765
X-RAY DIFFRACTIONf_angle_d1.4882400
X-RAY DIFFRACTIONf_chiral_restr0.055269
X-RAY DIFFRACTIONf_plane_restr0.008319
X-RAY DIFFRACTIONf_dihedral_angle_d15.216659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2529-2.47880.3011250.25512805293096
2.4788-2.83560.28781470.24632740288795
2.8356-3.56570.32081400.23362800294094
3.5657-15.69310.27661280.19072520264886
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)
11.60440.6878-0.60240.3371-0.41221.9620.1437-0.03850.017-0.3051-0.1328-0.02950.12910.3278-0.09470.36750.05930.04030.1034-0.00930.146410.83816.85438.8493
20.94950.37430.20472.4122-0.43641.65640.15560.20110.3479-0.406-0.0390.2041-0.2627-0.0859-0.09560.2871-0.02910.06080.1693-0.0180.13824.424230.11138.3973
32.0956-0.3116-0.50761.1282-0.08572.25140.335-0.30840.25720.0141-0.1546-0.0131-0.21770.3006-0.09580.2018-0.03950.01480.112-0.01270.15329.119324.095115.6561
40.7936-0.29340.08921.5272-0.89171.560.12920.0041-0.0649-0.5916-0.01610.22130.060.04420.33480.33150.0301-0.07950.21890.00630.03383.295415.88739.3497
50.94050.85921.30061.2080.81452.12-0.0312-0.51230.01820.1830.153-0.1276-0.3007-0.0872-0.050.27510.0298-0.01060.3067-0.07860.139616.787410.923134.0479
62.547-0.8312-0.23590.8658-0.36032.15790.0018-0.2065-0.5370.26320.1527-0.1516-0.16480.2274-0.09150.13550.02180.00570.3006-0.0070.116929.75094.766233.9077
71.93530.3840.38941.31980.08551.5667-0.44560.0550.04860.03580.40620.0562-0.18090.44110.06720.18890.0298-0.00550.203-0.04550.135123.05079.68326.7705
80.90030.81320.61971.16780.53581.508-0.0081-0.4351-0.24050.0799-0.107-0.09850.0228-0.09460.19080.1961-0.01930.08710.35840.05980.097515.68693.756232.7558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 93)A0
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 120 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 153 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 60 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 61 through 93 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 120 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 153 )B0

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