8vui

Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor

Method: X-RAY DIFFRACTION D_max: 114.1 Å Quality: GOOD

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

Erythropoietin receptor

Homo sapiens

UniProt P19235

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 25–250	Not recorded	S1CE VARIANT OF FAB-EPR-1 heavy chain × 1 S1CE VARIANT OF FAB-EPR-1 light chain × 1 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 4 CL CHLORIDE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CIT CITRIC ACID × 1 NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.2；298 K；0.2 M Ammonium Citrate dibasic, 20% PEG2000 monomethyl ether, pH 5.2	Resolution 2.10 Å R-free 0.240

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 8VUI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CN4 ERYTHROPOIETIN COMPLEXED WITH EXTRACELLULAR DOMAINS OF ERYTHROPOIETIN RECEPTOR Deposited 1999-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–249（225 aa） Fragment：EXTRACELLULAR LIGAND BINDING DOMAINS Chain B 25–249（225 aa） Fragment：EXTRACELLULAR LIGAND BINDING DOMAINS	Mutation：N52Q, N164Q, A211E Mutation：N52Q, N164Q, A211E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.80 Å R-free 0.336
1EBA COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN INACTIVE PEPTIDE [EMP33] CONTAINS 3,5-DIBROMOTYROSINE IN POSITION 4 (DENOTED DBY) Deposited 1998-10-02	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 A 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.70 Å R-free 0.299
1EBA COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN INACTIVE PEPTIDE [EMP33] CONTAINS 3,5-DIBROMOTYROSINE IN POSITION 4 (DENOTED DBY) Deposited 1998-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.70 Å R-free 0.299
1EBA COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN INACTIVE PEPTIDE [EMP33] CONTAINS 3,5-DIBROMOTYROSINE IN POSITION 4 (DENOTED DBY) Deposited 1998-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–248（215 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.70 Å R-free 0.299
1EBP COMPLEX BETWEEN THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] AND AN AGONIST PEPTIDE [EMP1] Deposited 1996-05-07	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 A 34–244（211 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–244（211 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.334
1EER CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPTOR AT 1.9 ANGSTROMS Deposited 1998-07-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 31–250（220 aa） Fragment：EXTRACELLULAR DOMAIN Chain C 31–250（220 aa） Fragment：EXTRACELLULAR DOMAIN	Mutation：N52Q, N164Q, A211E Mutation：N52Q, N164Q, A211E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.90 Å R-free 0.318
1ERN NATIVE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF ERYTHROPOIETIN (EPO) RECEPTOR [EBP] Deposited 1999-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–246（213 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 34–246（213 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.7；pH 7.7	Resolution 2.40 Å R-free 0.295
2JIX Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor Deposited 2007-07-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 25–249（225 aa） Fragment：EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.323
2JIX Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor Deposited 2007-07-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 25–249（225 aa） Fragment：EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.323
2JIX Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor Deposited 2007-07-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 25–249（225 aa） Fragment：EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.323
2MV6 Solution structure of the transmembrane domain and the juxta-membrane domain of the Erythropoietin Receptor in micelles Deposited 2014-09-23	Different construct 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 237–284（48 aa） Fragment：UNP residues 237-284	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；313 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 20 mM sodium phosphate, 10 v/v D2O, 250 mM DPC, 0.5 mM [U-99% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] protein, 10 % D2O, 20 mM sodium phosphate, 200-400 mM DPC, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4Y5V Diabody 305 complex with EpoR Deposited 2015-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 32–249（218 aa） Chain F 32–249（218 aa）	Mutation：N52Q, N164Q Mutation：N52Q, N164Q	GOL GLYCEROL × 10 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；HEPES, PEG 4000	Resolution 2.60 Å R-free 0.229
4Y5V Diabody 305 complex with EpoR Deposited 2015-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 32–249（218 aa）	Mutation：N52Q, N164Q	GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；HEPES, PEG 4000	Resolution 2.60 Å R-free 0.229
4Y5X Diabody 305 complex with EpoR Deposited 2015-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 32–249（218 aa） Chain L 32–249（218 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 12 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；sodium citrate, PEG 8000	Resolution 3.15 Å R-free 0.241
4Y5X Diabody 305 complex with EpoR Deposited 2015-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 32–249（218 aa） Chain I 32–249（218 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；sodium citrate, PEG 8000	Resolution 3.15 Å R-free 0.241
4Y5Y Diabody 330 complex with EpoR Deposited 2015-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 32–249（218 aa） Chain F 32–249（218 aa）	Mutation：N76Q, N188Q, D247L, and L248D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N76Q, N188Q, D247L, and L248D Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；Magnesium chloride, Tris, PEG 8000	Resolution 2.85 Å R-free 0.241
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6E2Q Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor Deposited 2018-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 273–338（66 aa） Fragment：UNP residues 273-338	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277.15 K；100 mM Tris, pH 7.6, 2-4% PEG8000	Resolution 2.65 Å R-free 0.263
6MOE Monomeric DARPin E2 complex with EpoR Deposited 2018-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 32–249（218 aa）	Not recorded	PO4 PHOSPHATE ION × 5 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；295 K；1 M sodium potassium phosphate pH 5.6 Cryoprotected in 25% ethylene glycol	Resolution 2.09 Å R-free 0.230
6MOE Monomeric DARPin E2 complex with EpoR Deposited 2018-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 32–249（218 aa）	Not recorded	PO4 PHOSPHATE ION × 4 EDO 1,2-ETHANEDIOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；295 K；1 M sodium potassium phosphate pH 5.6 Cryoprotected in 25% ethylene glycol	Resolution 2.09 Å R-free 0.230
6MOF Monomeric DARPin G2 complex with EpoR Deposited 2018-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–249（218 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；0.2 M Magnesium chloride, 0.1 M Tris pH 7.0, 10% PEG 8000, 25% ethylene glycol as cryoprotectant	Resolution 2.89 Å R-free 0.266
6MOH Dimeric DARPin C_R3 complex with EpoR Deposited 2018-10-04	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 32–249（218 aa） Chain D 32–249（218 aa）	Not recorded	PO4 PHOSPHATE ION × 7 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；295 K；0.1 M HEPES pH 7.3, 1.4 M sodium potassium phosphate, 24% glycerol cryoprotectant	Resolution 3.20 Å R-free 0.277
6MOI Dimeric DARPin C_angle_R5 complex with EpoR Deposited 2018-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 32–249（218 aa）	Not recorded	SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 20 MG MAGNESIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.3 M magnesium sulfate, 0.1 M bis-tris propane pH 7, 22.5% PurePEGs cocktail (Anatrace), 30% ethylene glycol cryoprotectant	Resolution 2.06 Å R-free 0.251
6MOJ Dimeric DARPin A_angle_R5 complex with EpoR Deposited 2018-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 32–249（218 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 6 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M sodium potassium tartrate, 0.1 M bis-tris propane pH 8.5, 20% PEG 3350, 30% glycerol as cryoprotectant	Resolution 2.43 Å R-free 0.250
6MOK Dimeric DARPin A_distance_R7 complex with EpoR Deposited 2018-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 32–249（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350	Resolution 5.10 Å R-free 0.299
6MOL Monoextended DARPin M_R12 complex with EpoR Deposited 2018-10-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 32–249（218 aa） Chain C 32–249（218 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；Seeded from 0.2 M NaCl, 0.1 M CAPS pH 10.5, 20% PEG 8000 into 0.2 M ammonium tartrate and 20% PEG 3350, with 10% glycerol, 10% ethylene glycol as cryoprotectant	Resolution 3.16 Å R-free 0.260
8VVM Structure of FabS1CE1-EPR1-1 in complex with the erythropoietin receptor Deposited 2024-01-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 25–250（226 aa）	Mutation：residues 22-250	PEG DI(HYDROXYETHYL)ETHER × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；0.1 M MMT buffer pH 5.0, 25% PEG1500	Resolution 2.90 Å R-free 0.273
8VVO Structure of FabS1CE2-EPR1-1 in complex with the erythropoietin receptor Deposited 2024-01-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 25–250（226 aa）	Mutation：residues 22-250	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1 M MMT buffer pH 6.0, 25% PEG1500	Resolution 3.09 Å R-free 0.289

20 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EPOR_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–226； UniProt 25–250

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	8vui
Deposition date deposition_date	2024-01-29
Structure title title	Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor
Keywords keywords	proliferation, engineered antibody, high-affinity binding, enhanced crystallization, 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	32.71 Å
Radius of gyration Rg (electron density) rg_electron	32.97 Å
Forward intensity I(0) i0	73249600.00
Molecular weight molecular_weight	67508.0 kDa
Excluded volume excluded_volume	84165 Å³
Envelope volume envelope_volume	111160 Å³
Hydration-shell volume shell_volume	30971 Å³
Envelope diameter envelope_diameter	123.0 Å
Shell Rg shell_rg	36.18 Å
Envelope Rg envelope_rg	33.19 Å
Shape Rg shape_rg	32.95 Å
Total Rg total_rg	33.28 Å
Total atoms total_atoms	4749
Residues n_residues	626
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	114.1 Å
Rg (real space) rg_real	33.18 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	7.3250e+07
I(0) uncertainty (real space) i0_real_error	1.1650e+06
Rg (reciprocal space) rg_reciprocal	32.99 Å
I(0) (reciprocal space) i0_reciprocal	73240000.0000
Solution quality estimate total_estimate	0.7942
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.9 Å
Skewness Skewness skewness	0.609
Kurtosis Kurtosis kurtosis	-0.176
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8418000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.722; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.664; Smooth: 0.493

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	S1CE VARIANT OF FAB-EPR-1 heavy chain
Molecular weight formula_weight	24096.0 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	5016

EVQLVESGGGLVQPGGSLRLSCAASGFNLRSYYMHWVRQAPGKGLEWVASISPYYSYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARHGYGAMDYWGQGTLVTVFNQIKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	S1CE VARIANT OF FAB-EPR-1 light chain
Molecular weight formula_weight	23049.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYSLITFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVSWYVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Erythropoietin receptor
Molecular weight formula_weight	25680.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

APPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLDPHHHHHH

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 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 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

Entity 8 Entity 8 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	222

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8. Citations (1)

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Unit-cell length a length_a	56.390 Å
Unit-cell length b length_b	71.930 Å
Unit-cell length c length_c	197.020 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	98.510 Å
R factor r_factor	0.1991
R_work r_work	0.1973
R_free r_free	0.2398

fit	/app/data/saxs_computation/vu/8vui/8vui.fit
pddf	/app/data/pr_computation/vu/8vui/8vui.pr.out
profile	/app/data/saxs_computation/vu/8vui/8vui.dat

Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor

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

Erythropoietin receptor

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 (10)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)