SAXSdb — 6w16

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

Fusion glycoprotein F0,Envelope glycoprotein fusion

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 1–28	Not recorded	458 Fab heavy chain × 1 458 Fab light chain × 1 ;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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate	Resolution 3.10 Å R-free 0.234

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 6W16	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M7W Independently verified structure of gp41-M-MAT, a membrane associated MPER trimer from HIV-1 gp41 Deposited 2013-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–59（59 aa） Chain B 1–59（59 aa） Chain C 1–59（59 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Pressure ambient NMR sample composition 2 mM protein, 50 mM sodium phosphate, 100 mM [U-99% 2H] DPC, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5KWW Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein Deposited 2016-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain F 1–28（28 aa） Fragment：F0 (UNP residues 1-513) + Envelope glycoprotein (UNP residues 1-28)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 3 SO4 SULFATE ION × 30 6YA 3-[[5-chloranyl-1-(3-methylsulfonylpropyl)indol-2-yl]methyl]-1-[2,2,2-tris(fluoranyl)ethyl]imidazo[4,5-c]pyridin-2-one × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；1.54 M potassium/sodium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, pH 9.5	Resolution 2.50 Å R-free 0.239
5U68 Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus Deposited 2016-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–28（28 aa） Fragment：UNP P03420 residues 1-513,UNP M1E1E4 residues 1-28 Chain B 1–28（28 aa） Fragment：UNP P03420 residues 1-513,UNP M1E1E4 residues 1-28 Chain C 1–28（28 aa） Fragment：UNP P03420 residues 1-513,UNP M1E1E4 residues 1-28	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.1M Potassium Nitrate, 0.1M Citrate Phosphate pH 4.2, 1 % Tacsimate pH 7.0, 14 (w/v) % PEG 6000	Resolution 3.08 Å R-free 0.239
6A0Z Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, HA head region Deposited 2018-06-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289.15 K；0.1 M Bis-Tris-propane pH 6.5, 0.2 M NaAc and 18% (w/v) PEG 3350	Resolution 2.33 Å R-free 0.218
6APD Crystal structure of RSV F bound by AM22 and the infant antibody ADI-19425 Deposited 2017-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–29（29 aa） Chain B 1–29（29 aa） Chain C 1–29（29 aa）	Mutation：N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V Mutation：N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V Mutation：N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；10% PEG 4000 10% 2-propanol 0.1 M sodium citrate pH 5.5	Resolution 4.10 Å R-free 0.256
6CNV INFLUENZA B/BRISBANE HEMAGGLUTININ FAB CR9115 SD84H COMPLEX Deposited 2018-03-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain B 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；100 mM sodium acetate, pH 4.5, 5.5 M sodium formate, and 5% MPD	Resolution 4.10 Å R-free 0.276
6CXC 3.9A Cryo-EM structure of murine antibody bound at a novel epitope of respiratory syncytial virus fusion protein Deposited 2018-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–30（30 aa） Chain B 1–30（30 aa） Chain C 1–30（30 aa） Chain D 1–30（30 aa） Chain E 1–30（30 aa） Chain F 1–30（30 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.90 Å
6DC3 RSV prefusion F bound to RSD5 Fab Deposited 2018-05-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–28（28 aa）	Not recorded	SO4 SULFATE ION × 13 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M Lithium sulfate, 0.1 M Tris pH 8.0	Resolution 3.50 Å R-free 0.205
6DC5 RSV prefusion F in complex with AM22 Fab Deposited 2018-05-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5	Resolution 3.50 Å R-free 0.280
6DC5 RSV prefusion F in complex with AM22 Fab Deposited 2018-05-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5	Resolution 3.50 Å R-free 0.280
6DC5 RSV prefusion F in complex with AM22 Fab Deposited 2018-05-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5	Resolution 3.50 Å R-free 0.280
6G9I Crystal structure of Ebolavirus glycoprotein in complex with clomipramine Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 2–28（27 aa）	Mutation：H613A,H613A,H613A,H613A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 GOL GLYCEROL × 12 CXX 3-(3-CHLORO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；293 K；9% (w/v) PEG 6000 and 0.1 M Sodium citrate tribasic dihydrate	Resolution 2.19 Å R-free 0.208
6ONA Crystal structure of Influenza hemagglutinin from strain A/Hickox/JY2/1940 Deposited 2019-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–28（28 aa） Fragment：UNP residues 18-509 Chain B 1–28（28 aa） Fragment：UNP residues 18-509 Chain C 1–28（28 aa） Fragment：UNP residues 18-509	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 PEG DI(HYDROXYETHYL)ETHER × 7 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；287 K；0.1 uL 9.5 mg/mL SEC-purified InvbQ.18715.a.KN11.PD38349 in 2 5 mM Tris, pH 8.5, 150 mM sodium chloride + 0.1 uL mother liquor (0.1 M sodium citrate, pH 5.5, 0.1 M magnesium chloride, 34% PEG400), flash-frozen, crystal ID 308018c7 data set les6-6	Resolution 1.95 Å R-free 0.230
6OUS Structure of fusion glycoprotein from human respiratory syncytial virus Deposited 2019-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–28（28 aa） Chain D 1–28（28 aa） Chain F 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM Tris 8.5, 10% PEG 8000, 200 mM ammonium sulfate	Resolution 3.40 Å R-free 0.275
6OUS Structure of fusion glycoprotein from human respiratory syncytial virus Deposited 2019-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–28（28 aa） Chain J 1–28（28 aa） Chain L 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM Tris 8.5, 10% PEG 8000, 200 mM ammonium sulfate	Resolution 3.40 Å R-free 0.275
6VKC Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein Deposited 2020-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain F 1–28（28 aa）	Not recorded	CL CHLORIDE ION × 3 SO4 SULFATE ION × 18 R0J 3-{[5-chloro-1-(4,4,4-trifluorobutyl)-1H-imidazo[4,5-b]pyridin-2-yl]methyl}-1-cyclopropyl-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one × 3 TAR D(-)-TARTARIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.52M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5	Resolution 2.60 Å R-free 0.229
6VKD Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein Deposited 2020-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain F 1–28（28 aa）	Not recorded	R0P 1-cyclopropyl-3-({1-[3-(methylsulfonyl)propyl]-1H-pyrrolo[3,2-c]pyridin-2-yl}methyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one × 3 CL CHLORIDE ION × 3 SO4 SULFATE ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.64M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5	Resolution 2.50 Å R-free 0.229
6VKE Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein Deposited 2020-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain F 1–28（28 aa）	Not recorded	NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 3 R0S 4-(5-chloro-2-{[1-(3,4-dimethoxyphenyl)-2-oxo-1,2-dihydro-3H-imidazo[4,5-c]pyridin-3-yl]methyl}-1H-indol-1-yl)butanenitrile × 3 CL CHLORIDE ION × 6 SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.64M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5	Resolution 2.10 Å R-free 0.199
7AD1 Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(One up trimer) Deposited 2020-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–28（28 aa） Chain B 1–28（28 aa） Chain C 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
7FJN Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex with two T6 Fab Deposited 2021-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–28（28 aa） Chain B 1–28（28 aa） Chain C 1–28（28 aa）	Mutation：R682G,R683S,R685S,K968P,V969P,S305T Mutation：R682G,R683S,R685S,K968P,V969P,S305T Mutation：R682G,R683S,R685S,K968P,V969P,S305T	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
7KC1 Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA Deposited 2020-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–28（28 aa） Chain D 1–28（28 aa） Chain I 1–28（28 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
7L7F Cryo-EM structure of human ACE2 receptor bound to protein encoded by vaccine candidate BNT162b1 Deposited 2020-12-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–28（28 aa） Chain F 1–28（28 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
7MPG Cryo-EM structure of Prefusion-stabilized RSV F (DS-Cav1) in complex with Fab AM14 Deposited 2021-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–29（29 aa） Chain B 1–29（29 aa） Chain C 1–29（29 aa）	Mutation：S155C,S190F,V207L,S290C Mutation：S155C,S190F,V207L,S290C Mutation：S155C,S190F,V207L,S290C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7QTI SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global) Deposited 2022-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 1–30（30 aa） Chain D 1–30（30 aa） Chain K 1–30（30 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
7ZRV cryo-EM structure of omicron spike in complex with de novo designed binder, full map Deposited 2022-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–30（30 aa） Chain B 1–30（30 aa） Chain C 1–30（30 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8HFX Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with white-tailed deer ACE2 Deposited 2022-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–29（29 aa） Chain B 1–29（29 aa） Chain C 1–29（29 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
9BJM Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein Deposited 2024-04-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–28（28 aa）	Not recorded	A1APZ 1'-{[5-chloro-1-(4,4,4-trifluorobutyl)-1H-1,3-benzimidazol-2-yl]methyl}-1-(methanesulfonyl)spiro[azetidine-3,3'-indol]-2'(1'H)-one × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3M NaFormate	Resolution 2.07 Å R-free 0.203

24 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	M1E1E4_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain F； PDBConstruct 501–528； UniProt 1–28

Fusion glycoprotein F0,Envelope glycoprotein fusion

Human immunodeficiency virus 1

UniProt Q6W8S4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 1–101 Chain F； UniProt 112–489	Not recorded	458 Fab heavy chain × 1 458 Fab light chain × 1 ;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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate	Resolution 3.10 Å R-free 0.234

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 6W16	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9OS5 Human antibody Fab MPV498 bound to hMPV B2 post-fusion F Deposited 2025-05-23	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 × 12 PDB declaration: dodecameric	Chain A 19–483（465 aa） Chain B 19–483（465 aa） Chain C 19–483（465 aa） Chain D 19–483（465 aa） Chain E 19–483（465 aa） Chain F 19–483（465 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6W8S4_9MONO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain F； PDBConstruct 1–101； UniProt 1–101 Author chain F； PDBConstruct 108–485； UniProt 112–489

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6w16
Deposition date deposition_date	2020-03-03
Structure title title	Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458 Fab
Keywords keywords	antibody, F protein, IMMUNE SYSTEM; IMMUNE SYSTEM
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	39.37 Å
Radius of gyration Rg (electron density) rg_electron	39.56 Å
Forward intensity I(0) i0	127426000.00
Molecular weight molecular_weight	89319.0 kDa
Excluded volume excluded_volume	111240 Å³
Envelope volume envelope_volume	164450 Å³
Hydration-shell volume shell_volume	37783 Å³
Envelope diameter envelope_diameter	138.5 Å
Shell Rg shell_rg	40.98 Å
Envelope Rg envelope_rg	39.33 Å
Shape Rg shape_rg	39.51 Å
Total Rg total_rg	39.80 Å
Total atoms total_atoms	6265
Residues n_residues	818
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	136.0 Å
Rg (real space) rg_real	39.90 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	1.2750e+08
I(0) uncertainty (real space) i0_real_error	2.0330e+06
Rg (reciprocal space) rg_reciprocal	39.56 Å
I(0) (reciprocal space) i0_reciprocal	127400000.0000
Solution quality estimate total_estimate	0.5947
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.550
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0334
Highest regularization parameter α highest_alpha	12520000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.586; Smooth: 0.913

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Fusion glycoprotein F0,Envelope glycoprotein fusion
Molecular weight formula_weight	59100.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F
Atom count atom_count	6265

MSWKVMIIISLLITPQHGLKESYLEESCSTITEGYLSVLRTGWYTNVFTLEVGDVENLTCTDGPSLIKTELDLTKSALRELKTVSADQLAREEQIENPRQSKKRKRRVATAAAVTAGIAIAKTIRLESEVNAIKGALKTTNEAVSTLGNGVRVLATAVRELKEFVSKNLTSAINKNKCDIADLKMAVSFSQFNRRFLNVVRQFSDNAGITPAISLDLMTDAELARAVSYMPTSAGQIKLMLENRAMVRRKGFGILIGVYGSSVIYMVQLPIFGVIDTPCWIIKAAPSCSEKDGNYACLLREDQGWYCKNAGSTVYYPNEKDCETRGDHVFCDTAAGINVAEQSRECNINISTTNYPCKVSTGRHPISMVALSPLGALVACYKGVSCSIGSNRVGIIKQLPKGCSYITNQDADTVTIDNTVYQLSKVEGEQHVIKGRPVSSSFDPIRFPEDQFNVALDQVFESIENSQALVDQSNKILNSAEKGNTSGRENLYFQGGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGGTEGRHHHHHH

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	458 Fab heavy chain
Molecular weight formula_weight	23316.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QGKLVESGGGVIQPGRSLRLSCAASGFDFSRYGLHWVRQAPGKGLEWVAVIVYAGSNKYYADSVKGRFTISKDNSKNTMHLQMSDLRTEDTAVYYCARDQAFDLWGQGTMVTVSSASTKGPSVFPLAPSSKSTGGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

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 3 Entity 3 polymer

Description description	458 Fab light chain
Molecular weight formula_weight	23586.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPASLSASVGDRVTITCQASQGISRSVNWYQQKPGKAPKLLIFDASHLERGVPSRFSGSGYGTDFTFTISSLQPEDIATYYCQQYDNLRISFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 4 Entity 4 branched

Description description	;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	910.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 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	1

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6w16h_
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.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6w16l1
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	d6w16l2
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.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	6w16H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6w16H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6w16L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6w16L02
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	128.489 Å
Unit-cell length b length_b	128.489 Å
Unit-cell length c length_c	188.352 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	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	hexagonal

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	41.050 Å
R factor r_factor	0.1934
R_work r_work	0.1897
R_free r_free	0.2339

fit	/app/data/saxs_computation/w1/6w16/6w16.fit
pddf	/app/data/pr_computation/w1/6w16/6w16.pr.out
profile	/app/data/saxs_computation/w1/6w16/6w16.dat

Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458 Fab

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

Fusion glycoprotein F0,Envelope glycoprotein fusion

State in the Current Structure

Other States of the Same Protein in the Database

Fusion glycoprotein F0,Envelope glycoprotein fusion

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

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 branched

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)