7lbf

CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109

Method: ELECTRON MICROSCOPY D_max: 174.6 Å Quality: REASONABLE

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

Envelope glycoprotein H

Human cytomegalovirus (strain Merlin)

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 Heteromer Protein × 8 其他Polymer 3 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–715	Not recorded	Envelope glycoprotein L × 1 （F5HCH8） Envelope glycoprotein O × 1 （Q8BCU3） Isoform 3 of Platelet-derived growth factor receptor alpha × 1 （P16234） Fab 13H11 light chain × 1 Fab 13H11 heavy chain × 1 Fab MSL-109 light chain × 1 Fab MSL-109 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.80 Å

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 7LBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VOB Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 Deposited 2017-05-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–715（715 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；10% (wt/vol) PEG400 10% isopropanol 2% (wt/vol) benzamidine 0.1M Tris pH 8.2	Resolution 3.02 Å R-free 0.237
5VOC Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 - Low resolution dataset for initial phasing by SAD Deposited 2017-05-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–715（715 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；10% (wt/vol) PEG400 10% isopropanol 2% (wt/vol) benzamidine 0.1M Tris pH 8.2	Resolution 3.99 Å R-free 0.276
5VOD Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6 Deposited 2017-05-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–715（715 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；10% (wt/vol) PEG methyl ether 500 0.1 M MES pH 6.2 0.00001 M phenol	Resolution 5.90 Å R-free 0.299
5VOD Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6 Deposited 2017-05-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–715（715 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；10% (wt/vol) PEG methyl ether 500 0.1 M MES pH 6.2 0.00001 M phenol	Resolution 5.90 Å R-free 0.299
7LBE CryoEM structure of the HCMV Trimer gHgLgO in complex with neutralizing fabs 13H11 and MSL-109 Deposited 2021-01-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–715（715 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MAN alpha-D-mannopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.90 Å
7LBG CryoEM structure of the HCMV Trimer gHgLgO in complex with human Transforming growth factor beta receptor type 3 and neutralizing fabs 13H11 and MSL-109 Deposited 2021-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–715（715 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5 seconds before plunging	Resolution 2.60 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

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UniProt name	GH_HCMVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–715； UniProt 1–715

Envelope glycoprotein L

Human cytomegalovirus (strain Merlin)

UniProt F5HCH8

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 Heteromer Protein × 8 其他Polymer 3 PDB declaration: octameric（8） Consistent with protein copy count	Chain B； UniProt 1–278	Not recorded	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein O × 1 （Q8BCU3） Isoform 3 of Platelet-derived growth factor receptor alpha × 1 （P16234） Fab 13H11 light chain × 1 Fab 13H11 heavy chain × 1 Fab MSL-109 light chain × 1 Fab MSL-109 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.80 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7LBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7LBE CryoEM structure of the HCMV Trimer gHgLgO in complex with neutralizing fabs 13H11 and MSL-109 Deposited 2021-01-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 1–278（278 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MAN alpha-D-mannopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.90 Å
7LBG CryoEM structure of the HCMV Trimer gHgLgO in complex with human Transforming growth factor beta receptor type 3 and neutralizing fabs 13H11 and MSL-109 Deposited 2021-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–278（278 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5 seconds before plunging	Resolution 2.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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UniProt name	GL_HCMVM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–278； UniProt 1–278

Envelope glycoprotein O

Human cytomegalovirus

UniProt Q8BCU3

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 Heteromer Protein × 8 其他Polymer 3 PDB declaration: octameric（8） Consistent with protein copy count	Chain C； UniProt 1–464	Not recorded	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （F5HCH8） Isoform 3 of Platelet-derived growth factor receptor alpha × 1 （P16234） Fab 13H11 light chain × 1 Fab 13H11 heavy chain × 1 Fab MSL-109 light chain × 1 Fab MSL-109 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.80 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7LBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7LBE CryoEM structure of the HCMV Trimer gHgLgO in complex with neutralizing fabs 13H11 and MSL-109 Deposited 2021-01-07	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 1–464（464 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 MAN alpha-D-mannopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.90 Å
7LBG CryoEM structure of the HCMV Trimer gHgLgO in complex with human Transforming growth factor beta receptor type 3 and neutralizing fabs 13H11 and MSL-109 Deposited 2021-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–464（464 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5 seconds before plunging	Resolution 2.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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UniProt name	Q8BCU3_HCMV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–464； UniProt 1–464

Isoform 3 of Platelet-derived growth factor receptor alpha

Homo sapiens

UniProt P16234

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 Heteromer Protein × 8 其他Polymer 3 PDB declaration: octameric（8） Consistent with protein copy count	Chain D； UniProt 1–524	Not recorded	Envelope glycoprotein H × 1 （Q6SW67） Envelope glycoprotein L × 1 （F5HCH8） Envelope glycoprotein O × 1 （Q8BCU3） Fab 13H11 light chain × 1 Fab 13H11 heavy chain × 1 Fab MSL-109 light chain × 1 Fab MSL-109 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.80 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7LBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GRN Crystal structure of PDGFRA in Complex with WQ-C-159 Deposited 2016-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Fragment：UNP residues 550-696 and 769-973 Chain A 769–973（205 aa） Fragment：UNP residues 550-696 and 769-973	Not recorded	748 N-[2-(dimethylamino)ethyl]-N-[[4-[[4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]methyl]pyridine-3-carboxamide × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M KCl, 20% PEG 3350, pH 7.0	Resolution 1.77 Å R-free 0.179
5K5X Crystal structure of human PDGFRA Deposited 2016-05-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Fragment：UNP residues 550-696,769-973 Chain A 769–973（205 aa） Fragment：UNP residues 550-696,769-973	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES pH7.5, 1.6M (NH4)2SO4, 0.1M NaCl	Resolution 2.17 Å R-free 0.224
6A32 Crystal structure of PDGFRA kinase domain mutant T674I Deposited 2018-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris pH 5.5, 27% PEG 3350	Resolution 1.87 Å R-free 0.240
6JOI Crystal structure of PDGFRA T674I in complex with crenolanib by co-crystallization Deposited 2019-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	6T2 1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M NaCl, 0.1M Tris pH 8.0, 15% PEG 4000	Resolution 3.10 Å R-free 0.244
6JOJ Crystal structure of PDGFRA T674I in complex with crenolanib by soaking Deposited 2019-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Not recorded	6T2 1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH6.9, 1.6M (NH4)2SO4, 0.1M NaCl	Resolution 2.60 Å R-free 0.233
6JOK Crystal structure of PDGFRA in complex with sunitinib by soaking Deposited 2019-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Not recorded	B49 N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH6.9, 1.6M (NH4)2SO4, 0.1M NaCl	Resolution 3.80 Å R-free 0.282
6JOL Crystal structure of PDGFRA in complex with imatinib by co-crystallization Deposited 2019-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Not recorded	STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium citrate pH4.5, 20% PEG 4000	Resolution 1.90 Å R-free 0.236
7RAM Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex with PDGFRalpha Deposited 2021-07-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–524（524 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；300mM NaCl and 20mM HEPES7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8PQH PDGFRA T674I mutant kinase domain in complex with avapritinib Deposited 2023-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	9JI Avapritinib × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；10 mg/mL, 13% PEG3350, 200 mM KCl	Resolution 2.50 Å R-free 0.249
8PQI PDGFRA T674I mutant kinase domain in complex with avapritinib derivative 9 Deposited 2023-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	9OO (1~{S})-~{N}-ethyl-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-yl]piperazin-1-yl]pyrimidin-5-yl]ethanamine × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；5 mg/mL, 5% PEG3350, 200 mM KCl	Resolution 2.60 Å R-free 0.254
8PQJ PDGFRA wild-type kinase domain Deposited 2023-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；285.15 K；10 mg/mL, 15% PEG3350, 100 mM Bis-Tris-Propane, pH 7.5	Resolution 1.82 Å R-free 0.215
8PQK APO crystal structure of PDGFRA-T674I kinase domain Deposited 2023-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；10 mg/mL, 22% PEG3350, 100 mM Bis-Tris-Propane, pH 7.5	Resolution 2.00 Å R-free 0.222
9GZH PDGFRA-T674I in complex with covalent ponatinib derivative 19 Deposited 2024-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–973（424 aa）	Mutation：T674I	A1IRC 3-(2-imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-~{N}-[4-(propanoylamino)-3-(trifluoromethyl)phenyl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；5 mg/mL, 18% PEG3350, 100 mM KCl	Resolution 2.20 Å R-free 0.215

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PGFRA_HUMAN
Isoform	P16234-3
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–524； UniProt 1–524

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	7lbf
Deposition date deposition_date	2021-01-07
Structure title title	CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109
Keywords keywords	virus, receptor, complex, neutralizing antibody, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex; VIRAL PROTEIN/Immune System
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	56.36 Å
Radius of gyration Rg (electron density) rg_electron	56.97 Å
Forward intensity I(0) i0	694820000.00
Molecular weight molecular_weight	222390.0 kDa
Excluded volume excluded_volume	279180 Å³
Envelope volume envelope_volume	398540 Å³
Hydration-shell volume shell_volume	62569 Å³
Envelope diameter envelope_diameter	186.5 Å
Shell Rg shell_rg	52.20 Å
Envelope Rg envelope_rg	56.30 Å
Shape Rg shape_rg	56.93 Å
Total Rg total_rg	56.96 Å
Total atoms total_atoms	15656
Residues n_residues	1923
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	174.6 Å
Rg (real space) rg_real	56.92 Å
Rg uncertainty (real space) rg_real_error	1.94 Å
I(0) (real space) i0_real	6.9480e+08
I(0) uncertainty (real space) i0_real_error	1.4760e+07
Rg (reciprocal space) rg_reciprocal	55.84 Å
I(0) (reciprocal space) i0_reciprocal	693700000.0000
Solution quality estimate total_estimate	0.5721
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.6 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	-0.686
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33600000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 0.997; Sysdev: 0.041; Positv: 1.000; Valcen: 0.768; Smooth: 0.001

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5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	87311.3 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	15656

MRPGLPSYLIILAVCLFSHLLSSRYGAEAVSEPLDKAFHLLLNTYGRPIRFLRENTTQCTYNSSLRNSTVVRENAISFNFFQSYNQYYVFHMPRCLFAGPLAEQFLNQVDLTETLERYQQRLNTYALVSKDLASYRSFSQQLKAQDSLGEQPTTVPPPIDLSIPHVWMPPQTTPHGWTESHTTSGLHRPHFNQTCILFDGHDLLFSTVTPCLHQGFYLIDELRYVKITLTEDFFVVTVSIDDDTPMLLIFGHLPRVLFKAPYQRDNFILRQTEKHELLVLVKKDQLNRHSYLKDPDFLDAALDFNYLDLSALLRNSFHRYAVDVLKSGRCQMLDRRTVEMAFAYALALFAAARQEEAGAQVSVPRALDRQAALLQIQEFMITCLSQTPPRTTLLLYPTAVDLAKRALWTPNQITDITSLVRLVYILSKQNQQHLIPQWALRQIADFALKLHKTHLASFLSAFARQELYLMGSLVHSMLVHTTERREIFIVETGLCSLAELSHFTQLLAHPHHEYLSDLYTPCSSSGRRDHSLERLTRLFPDATVPATVPAALSILSTMQPSTLETFPDLFCLPLGESFSALTVSEHVSYIVTNQYLIKGISYPVSTTVVGQSLIITQTDSQTKCELTRNMHTTHSITVALNISLENCAFCQSALLEYDDTQGVINIMYMHDSDDVLFALDPYNEVVVSSPRTHYLMLLKNGTVLEVTDVVVDATDGTKLGPEQKLISEEDLNSAVDGSGLNDIFEAQKIEWHENLYFQGHHHHHHHH

来源 Source

来源生物 organism	Human cytomegalovirus (strain Merlin)
通用名 common_name	HHV-5
NCBI Class编号 ncbi_taxonomy_id	295027
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	30846.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MCRRPDCGFSFSPGPVILLWCCLLLPIVSSAAVSVAPTAAEKVPAECPELTRRCLLGEVFEGDKYESWLRPLVNVTGRDGPLSQLIRYRPVTPEAANSVLLDEAFLDTLALLYNNPDQLRALLTLLSSDTAPRWMTVMRGYSECGDGSPAVYTCVDDLCRGYDLTRLSYGRSIFTEHVLGFELVPPSLFNVVVAIRNEATRTNRAVRLPVSTAAAPEGITLFYGLYNAVKEFCLRHQLDPPLLRHLDKYYAGLPPELKQTRVNLPAHSRYGPQAVDAR

来源 Source

来源生物 organism	Human cytomegalovirus (strain Merlin)
通用名 common_name	HHV-5
NCBI Class编号 ncbi_taxonomy_id	295027
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein O
Molecular weight formula_weight	58298.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGRKEDMRSISKLFFIISLTVLLFSIINCKVVRPPGRYWLGTVLSTIGKQKLDKFKLEILKQLEREPYTKYFNMTRQHVKNLTMNMTQFPQYYILAGPIRNDSITYLWFDFYSTQLRKPAKYVYSQYNHTAKTITFRPPSCGTVPSMTCLSEMLNVSKRNDTGEQGCGNFTTFNPMFFNVPRWNTKLYVGPTKVNVDSQTIYFLGLTALLLRYAQRNCTHSFYLVNAMSRNLFRVPKYINGTKLKNTMRKLKRKQAPVKEQLEKKTKKSQSTTTPYFSYTTSTALNVTTNATYRVTTSAKRIPTSTIAYRPDSSFMKSIMATQLRDLATWVYTTLRYRNEPFCKPDRNRTAVSEFMKNTHVLIRNETPYTIYGTLDMSSLYYNETMSVENETASDNNETTPTSPSTRFQKTFIDPLWDYLDSLLFLDKIRNFSLQLPAYGNLTPPEHRRAVNLSTLNSLWWWLQGSENLYFQGSAWSHPQFEKGGGSGGGSGGGSAWSHPQFEK

来源 Source

来源生物 organism	Human cytomegalovirus
通用名 common_name	HHV-5
NCBI Class编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Isoform 3 of Platelet-derived growth factor receptor alpha
Molecular weight formula_weight	59154.7 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGTSHPAFLVLGCLLTGLSLILCQLSLPSILPNENEKVVQLNSSFSLRCFGESEVSWQYPMSEEESSDVEIRNEENNSGLFVTVLEVSSASAAHTGLYTCYYNHTQTEENELEGRHIYIYVPDPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTFTVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQWTYPGEVKGKGITMLEEIKVPSIKLVYTLTVPEATVKDSGDYECAARQATREVKEMKKVTISVHEKGFIEIKPTFSQLEAVNLHEVKHFVVEVRAYPPPRISWLKNNLTLIENLTEITTDVEKIQEIRYRSKLKLIRAKEEDSGHYTIVAQNEDAVKSYTFELLTQVPSSILDLVDDHHGSTGGQTVRCTAEGTPLPDIEWMICKDIKKCNNETSWTILANNVSNIITEIHSRDRSTVEGRVTFAKVEETIAVRCLAKNLLGAENRELKLVAPTLRSEDDDDK

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 5 Entity 5 polymer

Description description	Fab 13H11 light chain
Molecular weight formula_weight	25780.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MKKNIAFLLASMFVFSIATNAYADIQMTQSPSSLSASVGDRVTITCRASQGINNYLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTAFTLTILSLQPEDVATYYCQKYNSAPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Fab 13H11 heavy chain
Molecular weight formula_weight	26600.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MKKNIAFLLASMFVFSIATNAYAQVQLVQSGAEVKKPGASVKVSCKASGYTFTNYYIHWVRQAPGQGLEWMGIIHPSSGGTSYAQKFQGRVTMTRDTSTSTVSMDLSSLRSEDTAVYYCGRAFRILGLSDVFVNDWGQGTVVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

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	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Fab MSL-109 light chain
Molecular weight formula_weight	28355.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MKKNIAFLLASMFVFSIATNAYADIVMTQSPLSLSVTPGEPASISCRSSQSLLHTNGYNYLDWYVQKPGQSPQLLIYLASNRASGVPDRFSGSGSGTDFTLKISRVETEDVGVYYCMQALQIPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGLNDIFEAQKIEWHE

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	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Fab MSL-109 heavy chain
Molecular weight formula_weight	27547.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MKKNIAFLLASMFVFSIATNAYAEEQVLESGGGLVKPGGSLRLSCAASGFTFSPYSVFWVRQAPGKGLEWVSSINSDSTYKYYADSVKGRFTISRDNAENSIFLQMNSLRAEDTAVYYCARDRSYYAFSSGSLSDYYYGLDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

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	Escherichia coli

Entity 9 Entity 9 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 10 Entity 10 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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	1235.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	18

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d7lbfe_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d7lbfg_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

▶

8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	3560620

fit	/app/data/saxs_computation/lb/7lbf/7lbf.fit
pddf	/app/data/pr_computation/lb/7lbf/7lbf.pr.out
profile	/app/data/saxs_computation/lb/7lbf/7lbf.dat

CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109

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

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein L

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein O

State in the Current Structure

Other States of the Same Protein in the Database

Isoform 3 of Platelet-derived growth factor receptor alpha

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

Entity 8 Entity 8 polymer

Polymer Polymer

来源 Source

Entity 9 Entity 9 branched

Entity 10 Entity 10 branched

Entity 11 Entity 11 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)