PDB-4frw: Crystal structure of human nectin-4 extracellular fragment D1-D2

ID or keywords:

Entry

Database: PDB / ID: 4frw

Title

Crystal structure of human nectin-4 extracellular fragment D1-D2

Components

Poliovirus receptor-related protein 4

Keywords

CELL ADHESION / Immunoglobulin-like domain / Ig domain / viral entry receptor

Function / homology

Function and homology information

Nectin/Necl trans heterodimerization / negative regulation of natural killer cell mediated cytotoxicity / Adherens junctions interactions / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / adherens junction / virus receptor activity / receptor ligand activity / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Harrison, O.J. / Jin, X. / Brasch, J. / Shapiro, L.

Citation

Journal: 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

Deposition	Jun 26, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 22, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 5, 2012	Group: Database references
Revision 1.2	Sep 26, 2012	Group: Database references
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4frw.cif.gz	477.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4frw.ent.gz	399.7 KB	Display	PDB format
PDBx/mmJSON format	4frw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4frw_validation.pdf.gz	479.7 KB	Display	wwPDB validaton report
Full document	4frw_full_validation.pdf.gz	530.4 KB	Display
Data in XML	4frw_validation.xml.gz	48.7 KB	Display
Data in CIF	4frw_validation.cif.gz	65.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fr/4frw ftp://data.pdbj.org/pub/pdb/validation_reports/fr/4frw	HTTPS FTP

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Related structure data

Related structure data	4fmfC 4fmkC 4fn0C 4fomC 4fqpC 4fs0C 3alpS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4fn0-2 2ikb-d 2z0n-1 3kbt-2 3kbu-2 2q12-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#231 - Mar 2019 Measles Virus Proteins similarity (6) #204 - Dec 2016 PD-1 similarity (2) #20 - Aug 2001 Poliovirus and Rhinovirus similarity (3) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (2) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (3) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1)

Deposited unit

A: Poliovirus receptor-related protein 4

B: Poliovirus receptor-related protein 4

C: Poliovirus receptor-related protein 4

D: Poliovirus receptor-related protein 4

E: Poliovirus receptor-related protein 4

F: Poliovirus receptor-related protein 4

141 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Poliovirus receptor-related protein 4

defined by author
46.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Poliovirus receptor-related protein 4

C: Poliovirus receptor-related protein 4

defined by author
46.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: Poliovirus receptor-related protein 4

defined by author
46.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: Poliovirus receptor-related protein 4

F: Poliovirus receptor-related protein 4

defined by author
46.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.971, 142.809, 341.802
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	SER	SER	A	A	32 - 243	1 - 212
2	1	GLY	GLY	SER	SER	B	B	32 - 243	1 - 212
1	2	GLY	GLY	HIS	HIS	A	A	32 - 241	1 - 210
2	2	GLY	GLY	HIS	HIS	C	C	32 - 241	1 - 210
1	3	GLU	GLU	SER	SER	A	A	33 - 243	2 - 212
2	3	GLU	GLU	SER	SER	D	D	33 - 243	2 - 212
1	4	LEU	LEU	LEU	LEU	A	A	34 - 240	3 - 209
2	4	LEU	LEU	LEU	LEU	E	E	34 - 240	3 - 209
1	5	THR	THR	HIS	HIS	A	A	36 - 245	5 - 214
2	5	THR	THR	HIS	HIS	F	F	36 - 245	5 - 214
1	6	GLY	GLY	HIS	HIS	B	B	32 - 241	1 - 210
2	6	GLY	GLY	HIS	HIS	C	C	32 - 241	1 - 210
1	7	GLU	GLU	SER	SER	B	B	33 - 243	2 - 212
2	7	GLU	GLU	SER	SER	D	D	33 - 243	2 - 212
1	8	LEU	LEU	LEU	LEU	B	B	34 - 240	3 - 209
2	8	LEU	LEU	LEU	LEU	E	E	34 - 240	3 - 209
1	9	THR	THR	HIS	HIS	B	B	36 - 244	5 - 213
2	9	THR	THR	HIS	HIS	F	F	36 - 244	5 - 213
1	10	GLU	GLU	HIS	HIS	C	C	33 - 241	2 - 210
2	10	GLU	GLU	HIS	HIS	D	D	33 - 241	2 - 210
1	11	LEU	LEU	LEU	LEU	C	C	34 - 240	3 - 209
2	11	LEU	LEU	LEU	LEU	E	E	34 - 240	3 - 209
1	12	THR	THR	VAL	VAL	C	C	36 - 242	5 - 211
2	12	THR	THR	VAL	VAL	F	F	36 - 242	5 - 211
1	13	LEU	LEU	LEU	LEU	D	D	34 - 240	3 - 209
2	13	LEU	LEU	LEU	LEU	E	E	34 - 240	3 - 209
1	14	THR	THR	HIS	HIS	D	D	36 - 244	5 - 213
2	14	THR	THR	HIS	HIS	F	F	36 - 244	5 - 213
1	15	THR	THR	HIS	HIS	E	E	36 - 241	5 - 210
2	15	THR	THR	HIS	HIS	F	F	36 - 241	5 - 210

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Poliovirus receptor-related protein 4 / Nectin-4 / Ig superfamily receptor LNIR / Processed poliovirus receptor-related protein 4 Mass: 23466.201 Da / Num. of mol.: 6 / Fragment: extracellular domain (D1-D2, UNP residues 32-243) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PVRL4, LNIR, PRR4 / Plasmid: pCEP4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q96NY8
Has protein modification	Y

#1: Protein

Poliovirus receptor-related protein 4 / Nectin-4 / Ig superfamily receptor LNIR / Processed poliovirus receptor-related protein 4

Mass: 23466.201 Da / Num. of mol.: 6 / Fragment: extracellular domain (D1-D2, UNP residues 32-243)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PVRL4, LNIR, PRR4 / Plasmid: pCEP4 / Cell line (production host): HEK 293F / Production host:

Homo sapiens (human) / References: UniProt: Q96NY8

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.73 Å³/Da / Density % sol: 66.99 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 3 M sodium chloride, 0.1 M Bis-Tris, pH 5.5, cryoprotectant: 30% w/v D-Trehalose, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2010

Radiation

Monochromator: cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 3.5→20 Å / Num. all: 26677 / Num. obs: 26677 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / R_sym value: 0.16 / Net I/σ(I): 7.8

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
3.5-3.56	5.5	2.4	0.57	1	100
3.56-3.62				1	99.6
3.62-3.69				1	100
3.69-3.77				1	99.5
3.77-3.85				1	100
3.85-3.94				1	100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ALP

3alp

Resolution: 3.5→20 Å / Cor.coef. F_o:F_c: 0.858 / Cor.coef. F_o:F_c free: 0.818 / SU B: 69.934 / SU ML: 0.5 / Cross valid method: THROUGHOUT / ESU R Free: 0.627 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2896	1334	5 %	RANDOM
R_work	0.25739	-	-	-
all	0.25898	26677	-	-
obs	0.25898	25301	98.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 93.892 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.18 Å²	0 Å²	0 Å²
2-	-	4.33 Å²	0 Å²
3-	-	-	-5.51 Å²

Refinement step

Cycle: LAST / Resolution: 3.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9257	0	0	0	9257

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	9484
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	6312
X-RAY DIFFRACTION	r_angle_refined_deg	1.649	1.971	12976
X-RAY DIFFRACTION	r_angle_other_deg	2.068	3.003	15416
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.703	5	1239
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.906	23.721	387
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.622	15	1394
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.577	15	69
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	1486
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	10725
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1788

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	6461	0.22
1	2	B	6461	0.22
2	1	A	6243	0.22
2	2	C	6243	0.22
3	1	A	5848	0.25
3	2	D	5848	0.25
4	1	A	5614	0.26
4	2	E	5614	0.26
5	1	A	4625	0.28
5	2	F	4625	0.28
6	1	B	6172	0.23
6	2	C	6172	0.23
7	1	B	5869	0.24
7	2	D	5869	0.24
8	1	B	5526	0.27
8	2	E	5526	0.27
9	1	B	4612	0.28
9	2	F	4612	0.28
10	1	C	5716	0.25
10	2	D	5716	0.25
11	1	C	5557	0.26
11	2	E	5557	0.26
12	1	C	4542	0.27
12	2	F	4542	0.27
13	1	D	5324	0.27
13	2	E	5324	0.27
14	1	D	4403	0.29
14	2	F	4403	0.29
15	1	E	4385	0.29
15	2	F	4385	0.29

LS refinement shell

Resolution: 3.5→3.592 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	70	-
R_work	0.286	1703	-
obs	-	-	98.99 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.3555	-1.6482	3.9156	7.6379	-7.353	9.1616	0.038	-0.0117	-0.7603	-0.1861	-0.0086	-0.4054	0.3994	-0.182	-0.0295	0.2038	-0.1068	0.1683	0.119	-0.1728	0.5201	8.4816	44.4411	-76.0469
2	5.4327	-0.7499	2.0079	4.3744	-2.0862	7.3153	-0.303	-0.9	0.1134	0.2632	-0.2426	-0.1788	-0.0969	0.7442	0.5456	0.146	0.0696	0.0158	0.5264	0.1387	0.3656	22.6776	17.6837	-45.4274
3	2.8631	-1.0606	-4.0451	4.2227	3.208	12.539	-0.2294	0.2594	0.239	0.1644	0.223	0.6428	-0.5228	-0.1665	0.0064	0.2097	0.042	-0.0602	0.1293	0.062	0.3113	22.251	-0.0449	-79.7938
4	4.1168	0.2694	-2.2181	0.9926	-0.5259	10.0805	-0.2864	-0.8265	-0.5135	0.2482	-0.0591	-0.1815	0.5406	0.7467	0.3455	0.3369	0.1958	0.0558	0.2829	0.1693	0.4227	5.9067	7.978	-40.9559
5	6.049	4.1425	6.6865	5.4402	4.6695	8.7868	-0.0902	-0.0664	0.4313	-0.1689	-0.165	0.3044	-0.228	-0.2813	0.2551	0.2966	0.0657	0.0916	0.1867	0.0829	0.2732	21.809	10.249	-102.865
6	6.4914	0.677	-0.4707	4.1698	-1.1704	6.1746	0.1105	-1.0864	0.5421	0.3403	-0.3027	-0.4854	-0.6694	0.736	0.1923	0.3438	-0.0079	-0.0382	0.3229	-0.0211	0.319	-5.812	27.812	-129.538
7	5.4857	2.8081	-4.3489	7.905	-4.7267	11.1196	0.3046	-0.066	-0.0076	1.0135	-0.4091	-0.2057	0.6838	0.2426	0.1044	0.587	0.0406	-0.0786	1.6385	0.475	0.5033	31.4552	3.5531	-12.0634
8	9.0329	2.4108	-3.4911	2.5715	-3.3654	10.0221	-0.0095	0.8378	0.5026	0.03	0.781	0.154	-0.7438	-1.554	-0.7715	0.312	0.3786	0.1304	1.0401	0.3488	0.5142	56.5463	21.4962	-41.7332
9	3.5438	-5.2869	4.3874	22.639	-10.0834	9.9878	0.259	-0.3361	-1.1959	-1.6383	-0.261	-0.0869	2.9966	0.1098	0.002	1.7045	0.2854	0.6423	0.7593	0.3895	1.0778	74.3331	-7.4225	-22.9677
10	3.7794	-1.9854	2.0289	7.3198	-2.9473	3.8691	-0.0149	-0.5757	1.119	0.561	0.5192	0.2985	-1.4462	-0.4588	-0.5043	1.1852	0.3382	0.5441	0.4658	-0.0537	0.7895	68.3957	32.6911	-30.149
11	3.0074	-1.0577	-3.0278	2.2803	-3.2648	13.0674	0.1579	-0.3032	0.0524	1.491	0.4285	0.0865	-3.2375	-0.265	-0.5864	3.0872	0.5401	-0.011	0.7933	-0.008	0.8186	66.107	-26.375	-4.565
12	3.4172	-0.4288	1.3372	4.401	-3.4662	3.1855	-0.5445	-0.1463	0.5673	0.5094	0.8769	1.0853	-0.7205	-0.5694	-0.3323	1.5878	0.9308	0.41	1.1703	0.3452	1.4053	48.085	-35.415	29.617

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	32 - 146
2	X-RAY DIFFRACTION	2	A	147 - 246
3	X-RAY DIFFRACTION	3	B	32 - 146
4	X-RAY DIFFRACTION	4	B	147 - 244
5	X-RAY DIFFRACTION	5	C	32 - 146
6	X-RAY DIFFRACTION	6	C	147 - 242
7	X-RAY DIFFRACTION	7	D	33 - 146
8	X-RAY DIFFRACTION	8	D	147 - 244
9	X-RAY DIFFRACTION	9	E	34 - 146
10	X-RAY DIFFRACTION	10	E	147 - 241
11	X-RAY DIFFRACTION	11	F	36 - 146
12	X-RAY DIFFRACTION	12	F	147 - 246

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