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- PDB-4fn0: Crystal structure of mouse nectin-2 extracellular fragment D1-D2,... -

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Basic information

Entry
Database: PDB / ID: 4fn0
TitleCrystal structure of mouse nectin-2 extracellular fragment D1-D2, 2nd crystal form
ComponentsPoliovirus receptor-related protein 2
KeywordsCELL ADHESION / Immunoglobulin-like domain / Ig domain / viral entry receptor
Function / homology
Function and homology information


cellular anatomical entity morphogenesis / Nectin/Necl trans heterodimerization / sperm mitochondrion organization / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / positive regulation of immunoglobulin mediated immune response / positive regulation of mast cell activation ...cellular anatomical entity morphogenesis / Nectin/Necl trans heterodimerization / sperm mitochondrion organization / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / spermatid nucleus differentiation / positive regulation of immunoglobulin mediated immune response / positive regulation of mast cell activation / regulation of viral entry into host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / acrosome assembly / Adherens junctions interactions / cilium organization / zonula adherens / cell-cell contact zone / fertilization / apical junction complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of T cell receptor signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / spermatid development / cell adhesion molecule binding / cytoskeleton organization / establishment of localization in cell / cell-cell junction / fusion of virus membrane with host plasma membrane / focal adhesion / cell surface / protein homodimerization activity / extracellular exosome / identical protein binding / plasma membrane
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 / Immunoglobulin-like domain superfamily ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsHarrison, O.J. / 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 18, 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 2
B: Poliovirus receptor-related protein 2
C: Poliovirus receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6459
Polymers74,7603
Non-polymers3,8856
Water28816
1
A: Poliovirus receptor-related protein 2
hetero molecules

A: Poliovirus receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7716
Polymers49,8402
Non-polymers2,9314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
2
B: Poliovirus receptor-related protein 2
C: Poliovirus receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2596
Polymers49,8402
Non-polymers2,4194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.022, 117.022, 158.467
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISAA32 - 2511 - 220
21HISHISBB32 - 2511 - 220
12ARGARGAA32 - 2491 - 218
22ARGARGCC32 - 2491 - 218
13ARGARGBB32 - 2491 - 218
23ARGARGCC32 - 2491 - 218

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Poliovirus receptor-related protein 2 / Nectin-2 / Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Murine herpes ...Nectin-2 / Herpes virus entry mediator B / Herpesvirus entry mediator B / HveB / Murine herpes virus entry protein B / mHveB / Poliovirus receptor homolog


Mass: 24920.076 Da / Num. of mol.: 3 / Fragment: extracellular domain (D1-D2, UNP residues 32-250)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pvrl2, Mph, Pvr, Pvs / Plasmid: pCEP4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P32507
#2: 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.: 5
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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.19 Å3/Da / Density % sol: 70.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% w/v PEG3350, 0.42 M sodium isothiocyanate, 0.1 M MES, pH 6.0, cryoprotectant: 15% 2R,3R-butane-di-ol, 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: 3.35→40 Å / Num. all: 18438 / Num. obs: 18438 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.09 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.35-3.475.740.54199.4
3.47-3.61199.8
3.61-3.77199.7
3.77-3.97199.8
3.97-4.22199.9
4.22-4.55199.9

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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 4FMK

4fmk


Resolution: 3.35→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.901 / SU B: 64.147 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.556 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29333 942 5.1 %RANDOM
Rwork0.24693 ---
obs0.24921 17484 99.26 %-
all-18438 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 135.057 Å2
Baniso -1Baniso -2Baniso -3
1-8.28 Å24.14 Å2-0 Å2
2--8.28 Å2-0 Å2
3----12.42 Å2
Refinement stepCycle: LAST / Resolution: 3.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 259 16 5383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195507
X-RAY DIFFRACTIONr_bond_other_d0.0060.023778
X-RAY DIFFRACTIONr_angle_refined_deg1.6432.0117542
X-RAY DIFFRACTIONr_angle_other_deg1.9943.0039067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1045656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05622.107242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.54815815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3261566
X-RAY DIFFRACTIONr_chiral_restr0.080.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215958
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021139
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.23 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A7178
12B7178
21A7101
22C7101
31B7130
32C7130
LS refinement shellResolution: 3.35→3.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 75 -
Rwork0.293 1132 -
obs--100 %
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)
14.53411.903-1.67474.01174.524819.4824-0.15260.218-0.43340.15230.20480.3393-0.3643-0.6357-0.05230.1570.0640.06420.06850.06690.2858-0.7274-7.50213.962
28.229-2.1549-0.82513.506910.698312.619-0.62732.941-3.1423-0.1216-0.51910.94422.3562-0.45821.14641.6341-0.50130.69271.4594-1.23371.999710.5493-33.7798-17.3563
35.49311.4588-3.69371.9912.800619.6282-0.44660.6433-0.2895-0.36040.40510.30740.71050.50540.04150.29930.1075-0.02890.62860.08750.415950.0151-33.2091-35.5983
414.732-4.8579-12.32844.58735.434613.7041-0.1873-0.88990.2165-0.16150.1673-0.3708-0.21090.78740.020.26890.2304-0.08350.3415-0.03650.493129.8417-17.6332-1.9353
52.61391.1242.02676.2591-3.876119.4272-0.1132-0.3870.37250.2990.08910.01020.1951-0.22730.02410.1328-0.13060.04440.9332-0.07040.360956.0856-25.8951-60.7712
63.4342-1.42812.95538.8628-9.503210.9684-1.5158-0.04291.88671.16042.60391.5092-2.2051-2.7891-1.08821.83211.23080.45182.89441.4212.939640.87270.1181-89.9061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 149
2X-RAY DIFFRACTION2A150 - 251
3X-RAY DIFFRACTION3B32 - 149
4X-RAY DIFFRACTION4B150 - 251
5X-RAY DIFFRACTION5C32 - 149
6X-RAY DIFFRACTION6C150 - 250

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