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- PDB-3hp3: Crystal structure of CXCL12 -

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Basic information

Entry
Database: PDB / ID: 3hp3
TitleCrystal structure of CXCL12
ComponentsCXCL12 protein
KeywordsCYTOKINE / Chemokine / CXCL12 / SDF
Function / homology
Function and homology information


chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / telencephalon cell migration / chemokine receptor binding / response to ultrasound / CXCL12-activated CXCR4 signaling pathway / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / telencephalon cell migration / chemokine receptor binding / response to ultrasound / CXCL12-activated CXCR4 signaling pathway / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / chemokine-mediated signaling pathway / cellular response to chemokine / positive regulation of monocyte chemotaxis / chemokine activity / Chemokine receptors bind chemokines / blood circulation / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / animal organ regeneration / positive regulation of T cell migration / detection of mechanical stimulus involved in sensory perception of pain / Nuclear signaling by ERBB4 / positive regulation of endothelial cell proliferation / positive regulation of cell adhesion / positive regulation of neuron differentiation / axon guidance / adult locomotory behavior / cell chemotaxis / growth factor activity / defense response / response to virus / response to peptide hormone / intracellular calcium ion homeostasis / neuron migration / chemotaxis / integrin binding / : / G alpha (i) signalling events / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region
Similarity search - Function
CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Stromal cell-derived factor 1 / Stromal cell-derived factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMurphy, J.W. / Lolis, E. / Xiong, Y. / Yuan, H. / Crichlow, G.
CitationJournal: Proteins / Year: 2009
Title: Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family
Authors: Murphy, J.W. / Yuan, H. / Kong, Y. / Xiong, Y. / Lolis, E.J.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 30, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CXCL12 protein
B: CXCL12 protein
C: CXCL12 protein
D: CXCL12 protein
E: CXCL12 protein
F: CXCL12 protein
G: CXCL12 protein
H: CXCL12 protein
I: CXCL12 protein
J: CXCL12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,16822
Polymers79,80510
Non-polymers2,36412
Water4,161231
1
A: CXCL12 protein
B: CXCL12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5525
Polymers15,9612
Non-polymers5913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-16 kcal/mol
Surface area7800 Å2
MethodPISA
2
C: CXCL12 protein
H: CXCL12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5525
Polymers15,9612
Non-polymers5913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-14 kcal/mol
Surface area8040 Å2
MethodPISA
3
D: CXCL12 protein
F: CXCL12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1583
Polymers15,9612
Non-polymers1971
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-12 kcal/mol
Surface area8160 Å2
MethodPISA
4
E: CXCL12 protein
G: CXCL12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5525
Polymers15,9612
Non-polymers5913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-21 kcal/mol
Surface area8260 Å2
MethodPISA
5
I: CXCL12 protein
hetero molecules

J: CXCL12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3554
Polymers15,9612
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1780 Å2
ΔGint-9 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.834, 117.468, 134.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31J
41D
51E
61F
71G
81H
91I
101C

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Components

#1: Protein
CXCL12 protein / Stromal cell-derived factor 1a / cDNA FLJ76575 / highly similar to Homo sapiens chemokine (C-X-C ...Stromal cell-derived factor 1a / cDNA FLJ76575 / highly similar to Homo sapiens chemokine (C-X-C motif) ligand 12 (stromalcell-derived factor 1) (CXCL12) / mRNA / Chemokine (C-X-C motif) ligand 12 (Stromal cell-derived factor 1) / isoform CRA_b


Mass: 7980.477 Da / Num. of mol.: 10 / Fragment: UNP residues 22-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, hCG_25667 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ICW0, UniProt: P48061*PLUS
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.5, 20% Jeffamine M-600, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.2→31 Å / Num. obs: 39406

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
REFMAC5.5.0093refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.18 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.748 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.245
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27995 709 2.1 %RANDOM
Rwork0.22832 ---
obs0.2294 33679 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 12 231 5222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225094
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9476933
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21823.965227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24815854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2251538
X-RAY DIFFRACTIONr_chiral_restr0.0870.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213797
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.28793201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.24595150
X-RAY DIFFRACTIONr_scbond_it8.48591893
X-RAY DIFFRACTIONr_scangle_it10.72691783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 408 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.785
Bloose positional0.845
Jloose positional0.695
Dloose positional0.835
Eloose positional0.695
Floose positional0.765
Gloose positional1.085
Hloose positional0.865
Iloose positional0.775
Cloose positional0.675
Aloose thermal6.2110
Bloose thermal6.3710
Jloose thermal5.1110
Dloose thermal5.7810
Eloose thermal5.9510
Floose thermal6.0510
Gloose thermal6.410
Hloose thermal6.4810
Iloose thermal5.3910
Cloose thermal4.4910
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 46 -
Rwork0.274 2351 -
obs--97.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.31454.06255.16792.96231.23945.81510.2836-0.3749-0.36190.0494-0.2154-0.44270.362-0.0304-0.06820.17740.0079-0.03860.116-0.05030.19376.6154.432-49.483
25.9629-0.26091.55214.31011.78365.69510.0570.1195-0.0504-0.1477-0.0231-0.4256-0.23570.399-0.03390.189-0.0515-0.03530.05810.01640.06227.48411.954-45.393
31.5186-1.5408-0.4155.9316-4.33735.59320.11170.06060.1246-0.4080.0213-0.01630.2384-0.2028-0.1330.1198-0.0142-0.02620.04560.00890.0214-9.4518.307-39.946
432.693-1.56937.68524.1619-1.90793.34060.42571.0945-0.0572-0.362-0.26710.105-0.12530.406-0.15860.2833-0.0750.06170.2213-0.10760.08651.91722.484-48.613
55.7616-2.71922.54947.4357-4.83184.3724-0.1596-0.4797-0.33420.46890.18940.0219-0.1767-0.2739-0.02980.1506-0.02260.0170.07050.02230.0249-7.5017.713-25.481
67.1101-0.24491.70169.6293-0.88636.62910.1324-0.2384-0.31430.7062-0.249-0.8639-0.2487-0.07770.11660.2012-0.0485-0.06130.10020.090.1407-3.0022.302-20.236
76.90890.9715-2.85381.10190.07753.9844-0.42540.591-0.3055-0.13590.2082-0.10170.2241-0.20030.21720.2203-0.06360.03390.1537-0.03970.02292.15922.835-14.034
855.043144.529-3.502431.7929-1.4602-3.2229-0.38140.1015-2.5564-0.62510.1382-1.97910.1493-0.0540.24321.88250.6181-0.2261.063-0.22060.81218.1410.946-21.813
95.39651.8498-4.81717.2779-2.65018.06690.0450.11130.11290.04460.20470.83640.2513-0.3822-0.24970.1046-0.0007-0.00990.10080.02010.0999-11.39319.4871.374
105.10021.9818-2.67867.232-2.63478.8901-0.3426-0.3078-0.5934-0.0495-0.1036-0.13230.8515-0.10170.44610.19430.01830.06990.06180.02810.0765-9.28313.6625.261
117.2853-2.813-3.62574.77615.62456.7596-0.20450.4029-0.6729-0.20540.3285-0.2456-0.13980.3852-0.1240.1866-0.05790.10860.1381-0.06790.25327.48316.57414.656
1238.6428-16.8818-6.28719.17830.3157-1.7021-0.0782-0.8584-0.1092-2.38120.86631.06681.5172-0.1517-0.78811.6118-0.4959-0.2780.5571-0.36961.39230.186.4034.25
135.1957-2.6813-3.90123.28291.46638.1015-0.2619-0.1471-0.2101-0.01290.03810.09050.03110.0310.22380.16550.0019-0.01340.00930.00810.0135-1.9923.1330.75
143.5358-2.27580.73066.0234-3.30126.7003-0.1929-0.3096-0.18290.25430.22660.4434-0.2435-0.4003-0.03370.11480.02960.00310.0837-0.00250.0438-7.13722.23537.871
154.47522.33481.57227.79432.73953.1832-0.21790.2549-0.3542-0.17780.0531-0.28130.0260.34670.16480.1367-0.00860.00520.05540.02810.08717.41810.56245.575
1610.4202-1.87984.78466.0915-3.74967.420.15670.1869-0.3178-0.3014-0.1347-0.0150.30780.4667-0.0220.1417-0.00560.0540.0447-0.03180.12341.985.69439.098
171.1315-0.2555-1.46697.50554.44094.35740.1579-0.3426-0.09230.5436-0.143-0.2829-0.00330.353-0.01490.228-0.0838-0.11280.2140.05490.092211.4619.84360.219
185.06331.3678-2.1445.13150.2373.98680.2874-0.37010.00430.8057-0.13730.4286-0.4453-0.0924-0.15010.3903-0.01750.05170.130.04880.07583.74523.56662.791
193.16192.22771.19662.4952-2.32215.6640.23510.25920.39310.06560.19680.5949-0.2978-0.4137-0.43190.28110.0048-0.04810.1393-0.00860.2511-4.7657.34869.431
206.2615-0.8306-1.95625.2572-2.286512.45230.17560.81980.6774-0.20140.59950.5069-0.2292-1.6417-0.77510.22140.0202-0.04670.38980.15670.1825-10.11210.26162.368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1I5 - 23
2X-RAY DIFFRACTION2I24 - 67
3X-RAY DIFFRACTION3G3 - 55
4X-RAY DIFFRACTION4G56 - 67
5X-RAY DIFFRACTION5E5 - 36
6X-RAY DIFFRACTION6E37 - 64
7X-RAY DIFFRACTION7B5 - 60
8X-RAY DIFFRACTION8B61 - 65
9X-RAY DIFFRACTION9A4 - 25
10X-RAY DIFFRACTION10A26 - 65
11X-RAY DIFFRACTION11C4 - 60
12X-RAY DIFFRACTION12C61 - 66
13X-RAY DIFFRACTION13H5 - 41
14X-RAY DIFFRACTION14H42 - 67
15X-RAY DIFFRACTION15D4 - 36
16X-RAY DIFFRACTION16D37 - 67
17X-RAY DIFFRACTION17F5 - 22
18X-RAY DIFFRACTION18F23 - 66
19X-RAY DIFFRACTION19J5 - 42
20X-RAY DIFFRACTION20J43 - 66

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