2j7z

Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha

Method: X-RAY DIFFRACTION D_max: 54.3 Å Quality: GOOD

▼

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

STROMAL CELL-DERIVED FACTOR 1 ALPHA

HOMO SAPIENS

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 22–89 Chain B； UniProt 22–89	Fragment：RESIDUES 22-89	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.95 Å R-free 0.247

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 2J7Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A15 SDF-1ALPHA Deposited 1997-12-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–88（67 aa） Chain B 22–88（67 aa）	Mutation：N33A Mutation：N33A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；PROTEIN CONCENTRATION 10MG/ML. WELL SOLUTION 1.9M AMMONIUM SULFATE 0.1M TRIS-HCL PH 8.5. CRYSTALLIZED USING VAPOR DIFFUSION., vapor diffusion	Resolution 2.20 Å R-free 0.298
1QG7 STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA) Deposited 1999-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–88（67 aa） Chain B 22–88（67 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.00 Å R-free 0.258
1SDF SOLUTION STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–88（67 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.9；303 K	Resolution not provided
1VMC STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA) Deposited 2004-09-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–89（68 aa） Fragment：SDF-1ALPHA (residues 22-89)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Ionic strength (raw mmCIF value) 50 mM SODIUM PHOSPHATE	Resolution not provided
2K01 Structure of a locked SDF1 dimer Deposited 2008-01-23	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain	Mutation：L36C,A65C Mutation：L36C,A65C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT NMR sample composition 0.620 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K03 Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21 Deposited 2008-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain	Mutation：L36C,A65C Mutation：L36C,A65C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT NMR sample composition .338 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .970 mM CXCR4, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.07 mM [U-100% 13C; U-100% 15N] CXCR4, 0.67 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K04 Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines Deposited 2008-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain	Mutation：L36C,A65C Mutation：L36C,A65C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT NMR sample composition .31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K05 Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21 Deposited 2008-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain	Mutation：L36C,A65C Mutation：L36C,A65C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT NMR sample composition .338 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .97 mM CXCR4, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.07 mM [U-100% 13C; U-100% 15N] CXCR4, 0.67 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KEC Structure of SDF-1/CXCL12 Deposited 2009-01-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–89（68 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT NMR sample composition 1.56 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KED Structure of SDF-1/CXCL12 Deposited 2009-01-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–89（68 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 0.001；Pressure AMBIENT NMR sample composition 1.6 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KEE Structure of SDF-1/CXCL12 Deposited 2009-01-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–89（68 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.001 mM；Pressure AMBIENT NMR sample composition 1.2 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KOL Solution structure of human SDF1-alpha H25R Deposited 2009-09-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–89（68 aa） Fragment：SDF-1-alpha, residues 22-89	Mutation：H25R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure AMBIENT NMR sample composition 3.3 mM [U-100% 13C; U-100% 15N] SDF1a H25R, 25 mM [U-99% 2H] MES, 0.02 % sodium azide, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N55 Structure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus Deposited 2015-07-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 22–89（68 aa）	Mutation：L76C, I79C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 2 mM [U-99% 13C; U-99% 15N] protein_1, 25 mM [U-2H] MES, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 2 mM protein_2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] protein_2, 25 mM [U-2H] MES, 0.02 % sodium azide, 10 % [U-99% 2H] D2O, 2 mM protein_1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NWG Structure of CXCL12:heparin disaccharide complex Deposited 2006-11-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–88（67 aa） Fragment：residues 22-88 Chain B 22–88（67 aa） Fragment：residues 22-88	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Soaking；pH 8.5；298 K；Grown in 2M Ammonium Sulfate, 0.1M TrisHCl pH 8.50. Soaked in 20 mM PEG-8000, 1M TrisHCl pH 8.5, 16 mM disaccharide. , Soaking, temperature 298K	Resolution 2.07 Å R-free 0.265
2SDF SOLUTION NMR STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), 30 STRUCTURES Deposited 1998-03-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–88（67 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.9；303 K	Resolution not provided
4LMQ Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12 Deposited 2013-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 29–89（61 aa） Fragment：UNP RESIDUES 29-89	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.2M NaF, 0.1M Bis-tris, propane, 23%w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.77 Å R-free 0.301
4LMQ Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12 Deposited 2013-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 29–89（61 aa） Fragment：UNP RESIDUES 29-89	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.2M NaF, 0.1M Bis-tris, propane, 23%w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.77 Å R-free 0.301
4UAI Crystal structure of CXCL12 in complex with inhibitor Deposited 2014-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 22–89（68 aa） Fragment：UNP residues 22-89 Chain B 22–89（68 aa） Fragment：UNP residues 22-89	Not recorded	3GG 1-phenyl-3-[4-(1H-tetrazol-5-yl)phenyl]urea × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2 M AmSO4, 2% MPD, 0.1 M MES Sodium Salt pH 6.5	Resolution 1.90 Å R-free 0.235
6SHR X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRODUCED SDF1-A Deposited 2019-08-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–89（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M tri-sodium citrate pH 5.6, 20 % (v/v) isopropanol and 20 % (w/v) PEG 4000	Resolution 1.75 Å R-free 0.239
7SK3 Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab Deposited 2021-10-19	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 × 6 PDB declaration: hexameric	Chain B 22–89（68 aa） Fragment：UNP residues 22-89	Not recorded	CLR CHOLESTEROL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7SK4 Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab Deposited 2021-10-19	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 × 6 PDB declaration: hexameric	Chain B 22–89（68 aa）	Mutation：N-terminus of CXCL12 (KPV) substituted with LRHQ	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7SK5 Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab Deposited 2021-10-19	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 × 5 PDB declaration: pentameric	Chain B 22–89（68 aa） Fragment：UNP residues 22-89	Not recorded	CLR CHOLESTEROL × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7SK6 Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ and an intracellular Fab Deposited 2021-10-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 22–89（68 aa）	Mutation：N-terminus of CXCL12 (KPV) substituted with LRHQ	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7SK7 Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab Deposited 2021-10-19	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 × 5 PDB declaration: pentameric	Chain B 22–89（68 aa） Fragment：UNP residues 22-89	Not recorded	GJ9 (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7SK8 Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, an extracellular Fab, and an intracellular Fab Deposited 2021-10-19	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 × 6 PDB declaration: hexameric	Chain B 22–89（68 aa） Fragment：UNP residues 22-89	Not recorded	CLR CHOLESTEROL × 6 LMN Lauryl Maltose Neopentyl Glycol × 1 GJ9 (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8K3Z Cryo-EM structure of CXCR4 in complex with CXCL12 Deposited 2023-07-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 22–83（62 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
8U4O Structure of CXCL12-bound CXCR4/Gi complex Deposited 2023-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 22–89（68 aa） Fragment：UNP residues 22-89	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9E82 ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7 Deposited 2024-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 25–89（65 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9ME1 hCXCR4-CXCL12 complex with 1:1 stoichiometry Deposited 2024-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain F 22–93（72 aa） Chain G 22–93（72 aa） Chain H 22–93（72 aa） Chain J 22–93（72 aa） Chain M 22–93（72 aa） Chain N 22–93（72 aa） Chain O 22–93（72 aa） Chain P 22–93（72 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MEU CXCR4 tetramer bound to 4 CXCL12 dimers Deposited 2024-12-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain F 22–93（72 aa） Chain G 22–93（72 aa） Chain H 22–93（72 aa） Chain J 22–93（72 aa） Chain M 22–93（72 aa） Chain N 22–93（72 aa） Chain O 22–93（72 aa） Chain P 22–93（72 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9UPU Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a Deposited 2025-04-29	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 × 6 PDB declaration: hexameric	Chain J 22–29（8 aa） Fragment：N-terminus	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9UPV Cryo-EM structure of CXCR4 complexed with agonist SDVX1 Deposited 2025-04-29	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 × 6 PDB declaration: hexameric	Chain J 22–29（8 aa） Fragment：N-terminus	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

31 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SDF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–68； UniProt 22–89 Author chain B； PDBConstruct 1–68； UniProt 22–89

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2j7z
Deposition date deposition_date	2006-10-18
Structure title title	Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha
Keywords keywords	GROWTH FACTOR, ALTERNATIVE SPLICING, CXCR4, CYTOKINE, REFOLDING, CHEMOTAXIS, SDF-1ALPHA; GROWTH FACTOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.44 Å
Radius of gyration Rg (electron density) rg_electron	15.22 Å
Forward intensity I(0) i0	4915400.00
Molecular weight molecular_weight	15945.0 kDa
Excluded volume excluded_volume	20182 Å³
Envelope volume envelope_volume	24711 Å³
Hydration-shell volume shell_volume	13743 Å³
Envelope diameter envelope_diameter	56.4 Å
Shell Rg shell_rg	21.06 Å
Envelope Rg envelope_rg	15.85 Å
Shape Rg shape_rg	15.21 Å
Total Rg total_rg	16.48 Å
Total atoms total_atoms	1118
Residues n_residues	136
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

▼

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

Maximum dimension Dmax dmax	54.3 Å
Rg (real space) rg_real	16.33 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	4.9150e+06
I(0) uncertainty (real space) i0_real_error	5.9040e+04
Rg (reciprocal space) rg_reciprocal	16.35 Å
I(0) (reciprocal space) i0_reciprocal	4915000.0000
Solution quality estimate total_estimate	0.7919
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.9 Å
Skewness Skewness skewness	0.182
Kurtosis Kurtosis kurtosis	-0.199
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	969800.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2j7za_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d2j7zb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (2 domains)

Domain ID domain_id	2j7zA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2j7zB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	35.215 Å
Unit-cell length b length_b	56.675 Å
Unit-cell length c length_c	71.629 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	8

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2133
R_work r_work	0.2133
R_free r_free	0.2466

Description description	STROMAL CELL-DERIVED FACTOR 1 ALPHA
Molecular weight formula_weight	7978.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1217

Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha

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

STROMAL CELL-DERIVED FACTOR 1 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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	HOMO SAPIENS
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

fit	/app/data/saxs_computation/j7/2j7z/2j7z.fit
pddf	/app/data/pr_computation/j7/2j7z/2j7z.pr.out
profile	/app/data/saxs_computation/j7/2j7z/2j7z.dat