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- PDB-4fqp: Crystal structure of human Nectin-like 5 full ectodomain (D1-D3) -

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Basic information

Entry
Database: PDB / ID: 4fqp
TitleCrystal structure of human Nectin-like 5 full ectodomain (D1-D3)
ComponentsPoliovirus receptor
KeywordsCELL ADHESION / Immunoglobulin-like domain / Ig domain / viral entry receptor
Function / homology
Function and homology information


susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / natural killer cell mediated cytotoxicity / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / natural killer cell mediated cytotoxicity / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / virus receptor activity / receptor ligand activity / focal adhesion / cell surface / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / 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: 3.6 Å
AuthorsHarrison, O.J. / Jin, X. / Brasch, J. / Shapiro, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Nectin ectodomain structures reveal a canonical adhesive interface.
Authors: Harrison, O.J. / Vendome, J. / Brasch, J. / Jin, X. / Hong, S. / Katsamba, P.S. / Ahlsen, G. / Troyanovsky, R.B. / Troyanovsky, S.M. / Honig, B. / Shapiro, L.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poliovirus receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1378
Polymers34,2671
Non-polymers3,8717
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.919, 138.919, 273.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Poliovirus receptor / Nectin-like protein 5 / NECL-5


Mass: 34266.602 Da / Num. of mol.: 1 / Fragment: ectodomain (D1-D3, UNP residues 28-334)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVR, PVS / Plasmid: pCEP4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P15151

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Sugars , 5 types, 7 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 11.12 Å3/Da / Density % sol: 88.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 55% v/v tacsimate, 0.1 M Bicine, pH 9.0, with additional 10% tacsimate as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: Bent single Si(111) crystal (horizontal focusing and deflection)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.563→40 Å / Num. all: 19387 / Num. obs: 19387 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rsym value: 0.11 / Net I/σ(I): 13.7
Reflection shellResolution: 3.563→3.73 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.55 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EOW

3eow
PDB Unreleased entry


Resolution: 3.6→20 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU B: 40.773 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.548 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27248 963 5.2 %RANDOM
Rwork0.24831 ---
all0.24953 19387 --
obs0.24953 17687 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.427 Å2
Baniso -1Baniso -2Baniso -3
1-6.81 Å23.4 Å20 Å2
2--6.81 Å2-0 Å2
3----10.21 Å2
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 257 0 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022685
X-RAY DIFFRACTIONr_bond_other_d0.0040.021751
X-RAY DIFFRACTIONr_angle_refined_deg1.7612.0713692
X-RAY DIFFRACTIONr_angle_other_deg3.0643.0034245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.04424.653101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40615371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5251513
X-RAY DIFFRACTIONr_chiral_restr0.4030.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212782
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02470
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 63 -
Rwork0.508 1034 -
obs--95.31 %
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)
12.09850.85140.81113.56136.03296.4049-0.23830.1184-0.25590.1706-0.25490.43380.1669-0.15370.49320.05660.00830.0750.0650.00070.1124-58.7149-19.0715-19.7168
20.16680.20160.676917.1127-2.19283.4617-0.03320.06050.05750.1539-0.1442-0.3769-0.08210.13410.17750.0439-0.0078-0.05280.20040.11730.1231-51.678520.6901-11.2038
33.329-4.56092.70789.1905-4.47046.9608-0.27940.33130.80320.956-0.3409-1.2082-0.95310.34820.62030.45210.0016-0.38440.04170.04850.5876-58.376763.3116-15.2561
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 142
2X-RAY DIFFRACTION2A143 - 241
3X-RAY DIFFRACTION3A242 - 333

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