4fqp

Crystal structure of human Nectin-like 5 full ectodomain (D1-D3)

Method: X-RAY DIFFRACTION D_max: 117.5 Å Quality: SUSPICIOUS

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Poliovirus receptor

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 6 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 28–334	Fragment：ectodomain (D1-D3, UNP residues 28-334)	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;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 ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;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 ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9；293.15 K；55% v/v tacsimate, 0.1 M Bicine, pH 9.0, with additional 10% tacsimate as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 3.60 Å R-free 0.272

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4FQP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DGI Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155 Deposited 1999-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-MERIC	Chain R 28–329（302 aa） Fragment：THREE EXTRACELLULAR DOMAINS OF CD155	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions ELECTRON MICROSCOPY RECONSTRUCTION；pH 7.5；WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION	Resolution 22.00 Å
1DGI Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155 Deposited 1999-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 28–329（302 aa） Fragment：THREE EXTRACELLULAR DOMAINS OF CD155	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions ELECTRON MICROSCOPY RECONSTRUCTION；pH 7.5；WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION	Resolution 22.00 Å
1DGI Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155 Deposited 1999-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain R 28–329（302 aa） Fragment：THREE EXTRACELLULAR DOMAINS OF CD155	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions ELECTRON MICROSCOPY RECONSTRUCTION；pH 7.5；WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION	Resolution 22.00 Å
1DGI Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155 Deposited 1999-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain R 28–329（302 aa） Fragment：THREE EXTRACELLULAR DOMAINS OF CD155	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions ELECTRON MICROSCOPY RECONSTRUCTION；pH 7.5；WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION	Resolution 22.00 Å
1DGI Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155 Deposited 1999-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 28–329（302 aa） Fragment：THREE EXTRACELLULAR DOMAINS OF CD155	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions POLIOVIRUS WAS INCUBATED WITH CD155-AP FOR 1 HOURS AT 4 DEGREES CELSIUS (277 KELVIN) USING A EIGHT-FOLD EXCESS OF CD155-AP FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. X-ray crystallization conditions ELECTRON MICROSCOPY RECONSTRUCTION；pH 7.5；WARNING: THIS IS AN ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE FORM OF REMARK 250 RECORDS AT THE TOP OF THE PDB COORDINATE FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION	Resolution 22.00 Å
1NN8 CryoEM structure of poliovirus receptor bound to poliovirus Deposited 2003-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC	Chain R 28–329（302 aa） Chain S 28–329（302 aa） Chain T 28–329（302 aa）	Not recorded	MYR MYRISTIC ACID × 60	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 15.00 Å
1NN8 CryoEM structure of poliovirus receptor bound to poliovirus Deposited 2003-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain R 28–329（302 aa） Chain S 28–329（302 aa） Chain T 28–329（302 aa）	Not recorded	MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 15.00 Å
1NN8 CryoEM structure of poliovirus receptor bound to poliovirus Deposited 2003-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain R 28–329（302 aa） Chain S 28–329（302 aa） Chain T 28–329（302 aa）	Not recorded	MYR MYRISTIC ACID × 5	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 15.00 Å
1NN8 CryoEM structure of poliovirus receptor bound to poliovirus Deposited 2003-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain R 28–329（302 aa） Chain S 28–329（302 aa） Chain T 28–329（302 aa）	Not recorded	MYR MYRISTIC ACID × 6	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 15.00 Å
1NN8 CryoEM structure of poliovirus receptor bound to poliovirus Deposited 2003-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain R 28–329（302 aa） Chain S 28–329（302 aa） Chain T 28–329（302 aa）	Not recorded	MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 15.00 Å
3EPC CryoEM structure of poliovirus receptor bound to poliovirus type 1 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-MERIC	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 60 MYR MYRISTIC ACID × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
3EPC CryoEM structure of poliovirus receptor bound to poliovirus type 1 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
3EPC CryoEM structure of poliovirus receptor bound to poliovirus type 1 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 5 MYR MYRISTIC ACID × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
3EPC CryoEM structure of poliovirus receptor bound to poliovirus type 1 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 6 MYR MYRISTIC ACID × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
3EPC CryoEM structure of poliovirus receptor bound to poliovirus type 1 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
3EPD CryoEM structure of poliovirus receptor bound to poliovirus type 3 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-MERIC	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 60 MYR MYRISTIC ACID × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPD CryoEM structure of poliovirus receptor bound to poliovirus type 3 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPD CryoEM structure of poliovirus receptor bound to poliovirus type 3 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 5 MYR MYRISTIC ACID × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPD CryoEM structure of poliovirus receptor bound to poliovirus type 3 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 6 MYR MYRISTIC ACID × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPD CryoEM structure of poliovirus receptor bound to poliovirus type 3 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SPH SPHINGOSINE × 1 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPF CryoEM structure of poliovirus receptor bound to poliovirus type 2 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-MERIC	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SC4 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE × 60 MYR MYRISTIC ACID × 60	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPF CryoEM structure of poliovirus receptor bound to poliovirus type 2 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SC4 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE × 1 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPF CryoEM structure of poliovirus receptor bound to poliovirus type 2 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SC4 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE × 5 MYR MYRISTIC ACID × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPF CryoEM structure of poliovirus receptor bound to poliovirus type 2 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SC4 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE × 6 MYR MYRISTIC ACID × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3EPF CryoEM structure of poliovirus receptor bound to poliovirus type 2 Deposited 2008-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 30–242（213 aa） Fragment：Poliovirus receptor CD155 D1D2	Mutation：N105D, N120S, N188Q, N218Q, N237S	SC4 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE × 1 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10mM Tris-HCl, 20mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3J8F Cryo-EM reconstruction of poliovirus-receptor complex Deposited 2014-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 300 PDB declaration: 300-meric	Chain 7 1–417（417 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60	ELECTRON MICROSCOPY cryo-EM buffer PBS；pH 7；PBS cryo-EM vitrification conditions Sample mixed and frozen within 2 minutes.；120 K；Cryogen ETHANE；Sample mixed and frozen within 2 minutes before plunging into liquid ethane.	Resolution 3.70 Å
3J8F Cryo-EM reconstruction of poliovirus-receptor complex Deposited 2014-10-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain 7 1–417（417 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer PBS；pH 7；PBS cryo-EM vitrification conditions Sample mixed and frozen within 2 minutes.；120 K；Cryogen ETHANE；Sample mixed and frozen within 2 minutes before plunging into liquid ethane.	Resolution 3.70 Å
3J8F Cryo-EM reconstruction of poliovirus-receptor complex Deposited 2014-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 25 PDB declaration: 25-meric	Chain 7 1–417（417 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer PBS；pH 7；PBS cryo-EM vitrification conditions Sample mixed and frozen within 2 minutes.；120 K；Cryogen ETHANE；Sample mixed and frozen within 2 minutes before plunging into liquid ethane.	Resolution 3.70 Å
3J8F Cryo-EM reconstruction of poliovirus-receptor complex Deposited 2014-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 30 PDB declaration: 30-meric	Chain 7 1–417（417 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer PBS；pH 7；PBS cryo-EM vitrification conditions Sample mixed and frozen within 2 minutes.；120 K；Cryogen ETHANE；Sample mixed and frozen within 2 minutes before plunging into liquid ethane.	Resolution 3.70 Å
3J8F Cryo-EM reconstruction of poliovirus-receptor complex Deposited 2014-10-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain 7 1–417（417 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer PBS；pH 7；PBS cryo-EM vitrification conditions Sample mixed and frozen within 2 minutes.；120 K；Cryogen ETHANE；Sample mixed and frozen within 2 minutes before plunging into liquid ethane.	Resolution 3.70 Å
3J9F Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C Deposited 2015-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 420 PDB declaration: 420-meric	Chain 7 28–143（116 aa） Fragment：SEE REMARK 999 Chain 8 142–243（102 aa） Fragment：SEE REMARK 999 Chain 9 242–333（92 aa） Fragment：SEE REMARK 999	Not recorded	PLM PALMITIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3J9F Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C Deposited 2015-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain 7 28–143（116 aa） Fragment：SEE REMARK 999 Chain 8 142–243（102 aa） Fragment：SEE REMARK 999 Chain 9 242–333（92 aa） Fragment：SEE REMARK 999	Not recorded	PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3J9F Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C Deposited 2015-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 7 28–143（116 aa） Fragment：SEE REMARK 999 Chain 8 142–243（102 aa） Fragment：SEE REMARK 999 Chain 9 242–333（92 aa） Fragment：SEE REMARK 999	Not recorded	PLM PALMITIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3J9F Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C Deposited 2015-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 42 PDB declaration: 42-meric	Chain 7 28–143（116 aa） Fragment：SEE REMARK 999 Chain 8 142–243（102 aa） Fragment：SEE REMARK 999 Chain 9 242–333（92 aa） Fragment：SEE REMARK 999	Not recorded	PLM PALMITIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3J9F Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C Deposited 2015-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain 7 28–143（116 aa） Fragment：SEE REMARK 999 Chain 8 142–243（102 aa） Fragment：SEE REMARK 999 Chain 9 242–333（92 aa） Fragment：SEE REMARK 999	Not recorded	PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
3UDW Crystal structure of the immunoreceptor TIGIT in complex with Poliovirus receptor (PVR/CD155/necl-5) D1 domain Deposited 2011-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–145（118 aa） Fragment：PVR, UNP residues 28-145 Chain D 28–145（118 aa） Fragment：PVR, UNP residues 28-145	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Ammonium acetate 0.1 M Bis-Tris pH 5.5 17% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.287
3URO Poliovirus receptor CD155 D1D2 Deposited 2011-11-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 29–243（215 aa） Fragment：poliovirus receptor CD155 D1D2 (UNP Residues 29-243)	Mutation：N105D, N120S, N188Q, N218Q, N237S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM MgSO4, 6.8 M NH4NO3, 100 mM Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.341
3URO Poliovirus receptor CD155 D1D2 Deposited 2011-11-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain R 29–243（215 aa） Fragment：poliovirus receptor CD155 D1D2 (UNP Residues 29-243)	Mutation：N105D, N120S, N188Q, N218Q, N237S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM MgSO4, 6.8 M NH4NO3, 100 mM Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.341
6ARQ Crystal structure of CD96 (D1) bound to CD155/necl-5 (D1-3) Deposited 2017-08-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 28–334（307 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；32% (v/v) Jeffamine ED-2001 0.1M HEPES pH7.3	Resolution 2.88 Å R-free 0.252
6ISC complex structure of mCD226-ecto and hCD155-D1 Deposited 2018-11-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–145（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris (pH 8.0), 0.15 M ammonium sulfate, and 15% (w/v) PEG4000	Resolution 2.20 Å R-free 0.265
6O3O Structure of human DNAM-1 (CD226) bound to nectin-like protein-5 (necl-5) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–334（307 aa） Chain D 28–334（307 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG3350, 0.18M K2SO4, 10mM EDTA	Resolution 2.80 Å R-free 0.231

12 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PVR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–307； UniProt 28–334

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4fqp
Deposition date deposition_date	2012-06-25
Structure title title	Crystal structure of human Nectin-like 5 full ectodomain (D1-D3)
Keywords keywords	Immunoglobulin-like domain, Ig domain, viral entry receptor, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.89 Å
Radius of gyration Rg (electron density) rg_electron	36.97 Å
Forward intensity I(0) i0	22906300.00
Molecular weight molecular_weight	37057.0 kDa
Excluded volume excluded_volume	46229 Å³
Envelope volume envelope_volume	68551 Å³
Hydration-shell volume shell_volume	18946 Å³
Envelope diameter envelope_diameter	125.5 Å
Shell Rg shell_rg	34.74 Å
Envelope Rg envelope_rg	36.73 Å
Shape Rg shape_rg	36.98 Å
Total Rg total_rg	36.73 Å
Total atoms total_atoms	2599
Residues n_residues	306
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	117.5 Å
Rg (real space) rg_real	36.66 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	2.2910e+07
I(0) uncertainty (real space) i0_real_error	3.7030e+05
Rg (reciprocal space) rg_reciprocal	36.19 Å
I(0) (reciprocal space) i0_reciprocal	22900000.0000
Solution quality estimate total_estimate	0.4008
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.7 Å
Skewness Skewness skewness	0.570
Kurtosis Kurtosis kurtosis	-0.642
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1017000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.346; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.079; Smooth: 0.007

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Poliovirus receptor
Molecular weight formula_weight	34266.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2599

DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVLAKPQNTAEVQKVQLTGEPVPMARCVSTGGRPPAQITWHSDLGGMPNTSQVPGFLSGTVTVTSLWILVPSSQVDGKNVTCKVEHESFEKPQLLTVNLTVYYPPEVSISGYDNNWYLGQNEATLTCDARSNPEPTGYNWSTTMGPLPPFAVAQGAQLLIRPVDKPINTTLICNVTNALGARQAELTVQVKEGPPHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	;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 ;
Molecular weight formula_weight	894.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	;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 ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4fqpA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4fqpA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4fqpA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	138.919 Å
Unit-cell length b length_b	138.919 Å
Unit-cell length c length_c	273.645 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2495
R_work r_work	0.2483
R_free r_free	0.2725

fit	/app/data/saxs_computation/fq/4fqp/4fqp.fit
pddf	/app/data/pr_computation/fq/4fqp/4fqp.pr.out
profile	/app/data/saxs_computation/fq/4fqp/4fqp.dat