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- PDB-4fmf: Crystal structure of human nectin-1 full ectodomain (D1-D3) -

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Basic information

Entry
Database: PDB / ID: 4fmf
TitleCrystal structure of human nectin-1 full ectodomain (D1-D3)
ComponentsPoliovirus receptor-related protein 1
KeywordsCELL ADHESION / Immunoglobulin-like domain / Ig domain / viral entry receptor
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
FORMIC ACID / Nectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 16, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _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_seq_id / _struct_conn.ptnr2_label_asym_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 1
B: Poliovirus receptor-related protein 1
C: Poliovirus receptor-related protein 1
D: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,64412
Polymers140,7624
Non-polymers1,8828
Water724
1
A: Poliovirus receptor-related protein 1
B: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3226
Polymers70,3812
Non-polymers9414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint7 kcal/mol
Surface area33540 Å2
MethodPISA
2
C: Poliovirus receptor-related protein 1
D: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3226
Polymers70,3812
Non-polymers9414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint8 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.288, 106.288, 334.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA36 - 3336 - 303
21ILEILEBB36 - 3336 - 303
12GLUGLUAA36 - 3356 - 305
22GLUGLUCC36 - 3356 - 305
13PROPROAA36 - 3376 - 307
23PROPRODD36 - 3376 - 307
14ILEILEBB36 - 3336 - 303
24ILEILECC36 - 3336 - 303
15ILEILEBB36 - 3336 - 303
25ILEILEDD36 - 3336 - 303
16GLUGLUCC36 - 3356 - 305
26GLUGLUDD36 - 3356 - 305

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 35190.547 Da / Num. of mol.: 4 / Fragment: extracellular domain (D1-D3, UNP residues 31-337)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVRL1, HVEC, PRR1 / Plasmid: pCEP4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q15223
#2: 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.: 4
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
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.8 M sodium formate, 0.1 M sodium citrate, pH 5.4, 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: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2010
RadiationMonochromator: cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 35252 / Num. obs: 34857 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.1 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.2-3.3142.20.51192.4
3.31-3.45198.9
3.45-3.6199.9
3.6-3.791100
3.79-4.031100
4.03-4.34199.9

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Processing

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

3alp


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.886 / SU B: 47.64 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25841 1749 5 %RANDOM
Rwork0.2328 ---
all0.23408 34902 --
obs0.23408 33089 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.238 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å21.66 Å2-0 Å2
2--3.31 Å2-0 Å2
3----4.97 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9470 0 124 4 9598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029823
X-RAY DIFFRACTIONr_bond_other_d0.0070.026616
X-RAY DIFFRACTIONr_angle_refined_deg1.651.96413380
X-RAY DIFFRACTIONr_angle_other_deg2.6033.00316078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.15951200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76924.333450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.911151601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2581564
X-RAY DIFFRACTIONr_chiral_restr0.0870.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110879
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021958
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101460.15
12B101460.15
21A104560.13
22C104560.13
31A103140.16
32D103140.16
41B102260.14
42C102260.14
51B102630.13
52D102630.13
61C103670.15
62D103670.15
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 141 -
Rwork0.313 2168 -
obs--91.05 %
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)
12.08241.6697-0.6613.8012-3.13364.0176-0.065-0.04660.01660.04560.12050.1244-0.0677-0.178-0.05560.02140.0469-0.01850.1145-0.05020.1784-22.84444.76-48.156
24.40051.68973.23462.26510.61556.5793-0.0028-0.22270.00650.19450.06180.2555-0.2734-0.4439-0.05910.07590.03710.09530.08070.0150.1515-19.83241.395-24.81
31.6009-1.3830.41073.1968-2.85853.9478-0.0205-0.0576-0.059-0.0740.09870.1677-0.0218-0.1203-0.07810.0472-0.02420.03110.0904-0.04630.2051-22.84516.639-54.125
42.053-1.2852-2.74672.74571.61637.34530.10210.21350.0225-0.186-0.07830.26860.3582-0.4545-0.02370.15310.0069-0.11560.1067-0.00840.181-19.95519.954-77.448
52.50860.4339-1.10636.7907-2.53063.44820.08760.33560.2196-0.18840.1065-0.0926-0.3697-0.0355-0.19420.1203-0.0295-0.02220.13840.00920.1511-6.70479.457-69.759
68.98372.51894.16133.40822.53065.09590.4991-0.3236-0.38820.5038-0.2248-0.50690.42160.3933-0.27440.3236-0.0292-0.03060.26850.14310.155816.9452.146-3.267
72.5618-0.78071.12556.9379-4.37345.30810.3015-0.1512-0.22480.1152-0.13030.03790.4290.0718-0.17120.1405-0.0132-0.0010.0704-0.00240.1066-6.759-18.126-32.674
87.8474-1.1327-2.73462.1850.66673.83830.17150.41130.1362-0.39090.0056-0.3713-0.16310.1696-0.1770.34450.02440.01090.27310.07750.122416.9479.428-98.888
910.81154.8056-6.26492.998-4.78328.6435-0.13471.89260.64170.17730.62020.4528-0.73790.0967-0.48561.4357-0.6291-0.08591.6980.30490.89677.308104.624-102.683
100.9803-1.47420.64452.7606-1.46170.8862-0.0663-0.83240.16380.71640.2525-0.0001-0.44520.4115-0.18632.2404-0.6781-0.613.1097-0.18451.519243.96160.17229.674
118.0276-6.07767.09045.4683-6.63859.2021-0.3371-1.5134-0.84320.36450.70960.4420.5046-0.3374-0.37260.92640.21220.00521.08440.32850.70736.527-43.987-0.265
124.4224-4.8899-3.77645.59264.78316.14880.54660.10330.354-0.42350.1497-0.32110.08841.1977-0.69631.02830.00550.29741.36730.07810.629546.4821.768-130.686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 143
2X-RAY DIFFRACTION2B36 - 143
3X-RAY DIFFRACTION3C36 - 143
4X-RAY DIFFRACTION4D36 - 143
5X-RAY DIFFRACTION5A144 - 244
6X-RAY DIFFRACTION5A401 - 402
7X-RAY DIFFRACTION6B144 - 244
8X-RAY DIFFRACTION6B401 - 402
9X-RAY DIFFRACTION7C144 - 244
10X-RAY DIFFRACTION7C401 - 402
11X-RAY DIFFRACTION8D144 - 244
12X-RAY DIFFRACTION8D401 - 402
13X-RAY DIFFRACTION9A245 - 337
14X-RAY DIFFRACTION10B245 - 334
15X-RAY DIFFRACTION11C245 - 336
16X-RAY DIFFRACTION12D245 - 337

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