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- PDB-6svl: human Myeloid-derived growth factor (MYDGF) in complex with neutr... -

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Basic information

Entry
Database: PDB / ID: 6svl
Titlehuman Myeloid-derived growth factor (MYDGF) in complex with neutralizing Fab
Components
  • Fab_heavy_chain
  • Fab_light_chain
  • Myeloid-derived growth factor
KeywordsCYTOKINE / MYDGF / growth factor / Fab / neutralizing antibody
Function / homology
Function and homology information


XBP1(S) activates chaperone genes / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / apoptotic process ...XBP1(S) activates chaperone genes / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Myeloid-derived growth factor / UPF0556 domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myeloid-derived growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsEbenhoch, R. / Nar, H.
CitationJournal: Nat Commun / Year: 2019
Title: Crystal structure and receptor-interacting residues of MYDGF - a protein mediating ischemic tissue repair.
Authors: Ebenhoch, R. / Akhdar, A. / Reboll, M.R. / Korf-Klingebiel, M. / Gupta, P. / Armstrong, J. / Huang, Y. / Frego, L. / Rybina, I. / Miglietta, J. / Pekcec, A. / Wollert, K.C. / Nar, H.
History
DepositionSep 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab_heavy_chain
B: Fab_light_chain
C: Myeloid-derived growth factor
D: Fab_heavy_chain
E: Fab_light_chain
F: Myeloid-derived growth factor
G: Fab_heavy_chain
H: Fab_heavy_chain
I: Fab_light_chain
J: Myeloid-derived growth factor
K: Fab_heavy_chain
L: Fab_light_chain
M: Fab_light_chain
N: Myeloid-derived growth factor
O: Fab_heavy_chain
P: Fab_light_chain
Q: Myeloid-derived growth factor
R: Myeloid-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,57521
Polymers408,29918
Non-polymers2763
Water46,9112604
1
A: Fab_heavy_chain
B: Fab_light_chain
C: Myeloid-derived growth factor


Theoretical massNumber of molelcules
Total (without water)68,0503
Polymers68,0503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fab_heavy_chain
E: Fab_light_chain
F: Myeloid-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1424
Polymers68,0503
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Fab_heavy_chain
I: Fab_light_chain
J: Myeloid-derived growth factor


Theoretical massNumber of molelcules
Total (without water)68,0503
Polymers68,0503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Fab_heavy_chain
L: Fab_light_chain
Q: Myeloid-derived growth factor


Theoretical massNumber of molelcules
Total (without water)68,0503
Polymers68,0503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: Fab_heavy_chain
M: Fab_light_chain
N: Myeloid-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1424
Polymers68,0503
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
O: Fab_heavy_chain
P: Fab_light_chain
R: Myeloid-derived growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1424
Polymers68,0503
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.519, 107.430, 109.369
Angle α, β, γ (deg.)71.540, 86.250, 73.380
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Fab_heavy_chain


Mass: 26561.465 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): HEK 293F
#2: Antibody
Fab_light_chain


Mass: 25633.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): HEK 293F
#3: Protein
Myeloid-derived growth factor / MYDGF


Mass: 15854.741 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYDGF, C19orf10 / Production host: Homo sapiens (human) / Strain (production host): HEK 293-6E / References: UniProt: Q969H8
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2604 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1 M trisodium citrate (pH 5.5) and 20 % PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.58→97.82 Å / Num. obs: 320264 / % possible obs: 63.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 24.26 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 10.2
Reflection shellResolution: 1.584→1.584 Å / Redundancy: 3 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 160008 / Rsym value: 0.633

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQW

1iqw


Resolution: 1.58→97.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.206 16013 5 %RANDOM
Rwork0.181 ---
obs0.182 320264 62.6 %-
Displacement parametersBiso max: 139.1 Å2 / Biso mean: 33.23 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.5024 Å20.9584 Å21.2789 Å2
2---1.2375 Å21.1692 Å2
3---2.7399 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.58→97.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24893 0 42 2604 27539
Biso mean--24.04 39.1 -
Num. residues----3231
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8458SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4293HARMONIC5
X-RAY DIFFRACTIONt_it25660HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact30213SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d25660HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg34917HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.09
X-RAY DIFFRACTIONt_other_torsion15.25
LS refinement shellResolution: 1.58→1.7 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2553 324 5.06 %
Rwork0.2162 6082 -
all0.2181 6406 -
obs--6.04 %
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)
14.3892-0.9441-0.75213.2763-0.46782.53620.20510.12621.133-0.04950.0332-0.0251-0.6031-0.1214-0.2383-0.14060.02820.0871-0.22970.0640.1197-70.865835.047629.6119
2-0.0024-0.60640.14751.7278-0.14890.58560.005-0.0489-0.04830.0589-0.0739-0.0639-0.10220.06340.0689-0.06230.01180.0195-0.02370.0238-0.0281-54.703160.59380.0328
30.87310.24350.17890.8876-0.37240.4573-0.027-0.08420.20310.0841-0.05260.0134-0.1088-0.01760.0795-0.0640.00430.0102-0.0448-0.0119-0.0126-37.431527.116425.6752
40.8405-0.3048-0.16963.7892-0.26111.10840.0563-0.0376-0.0543-0.079-0.01680.0697-0.31310.0065-0.0395-0.11490.04270.031-0.1302-0.035-0.1651-69.256670.5792-5.536
50.7386-0.02840.44060.67540.0410.4789-0.113-0.14640.16660.0582-0.0118-0.0651-0.1098-0.03350.1248-0.08010.0044-0.0154-0.0310.0087-0.0194-21.382221.427230.6924
64.8580.99840.95845.9851-0.14592.65520.06860.0265-0.7024-0.06640.04661.17450.4102-0.3332-0.1152-0.2805-0.05860.0118-0.2821-0.00250.2777-73.411621.40481.4411
72.41180.0671-1.03013.2146-0.33281.95950.0326-0.17720.0746-0.10130.0269-0.3507-0.22740.2172-0.0595-0.0907-0.02780.0302-0.09190.0078-0.0335-24.804847.7521-5.4879
80.6459-0.15860.10262.0556-0.40790.36630.03060.0205-0.0719-0.0097-0.06990.1053-0.00360.05120.0393-0.02810.03330.0241-0.01310.0299-0.026-26.426842.8303-35.6491
92.2528-0.22980.20364.3384-0.26511.84480.0680.0997-0.3601-0.1769-0.0547-0.12610.40260.0244-0.01330.03410.00830.0331-0.0130.01750.0452-44.417-17.969830.3783
100.6684-0.96630.18252.9486-0.80040.58170.11520.0904-0.1799-0.1197-0.10410.393-0.00540.0725-0.0112-0.14420.0273-0.0133-0.139-0.0042-0.0586-40.58953.2575-40.673
116.09970.64740.87695.2152-0.37352.46230.0869-0.2366-0.26650.043-0.00450.90540.291-0.3308-0.0823-0.2363-0.02070.0207-0.28560.04290.1709-47.47653.9571-34.3627
120.22720.0084-0.19721.2524-0.06280.2346-0.01240.03160.13580.0490.01540.1014-0.04090.004-0.003-0.03830.0439-0.0056-0.0245-0.0031-0.0087-106.6127-7.8766-33.4268
130.3015-0.3253-0.28841.3553-0.240.972-0.00610.0318-0.0406-0.1046-0.03370.21830.2688-0.02880.0398-0.02110.0065-0.0076-0.07690.0063-0.0687-46.17557.57951.7403
140.3770.0604-0.02991.66660.0470.3597-0.00780.03140.03950.0067-0.0101-0.08080.0197-0.03840.0179-0.03540.02750.0062-0.0546-0.0074-0.0472-93.6141-18.7985-40.3772
152.99260.3414-0.91313.4264-0.35371.37420.0086-0.13090.00520.04290.0107-0.4398-0.06940.1531-0.0193-0.13170.00590.0064-0.1394-0.01520.0372-85.740730.56-42.1849
160.6350.4405-0.19470.6602-0.02270.3701-0.01380.066-0.0762-0.0708-0.0293-0.08770.0611-0.01230.0431-0.05680.00430.01420.00860.0194-0.03-75.4156-8.596532.6892
170.3377-0.1139-0.17491.1962-0.29080.76030.04080.1487-0.0227-0.2905-0.11720.06250.34520.06150.07650.06020.07990.0154-0.1075-0.0097-0.1456-32.8751-0.0637-6.8048
180.83970.3323-0.20710.839-0.07980.4025-0.0566-0.004-0.1297-0.02650.0091-0.00880.14490.03760.0475-0.04950.00560.014-0.0330.0115-0.0446-91.3218-8.891941.8068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ N|* }N5 - 137
2X-RAY DIFFRACTION2{ A|* }A1 - 221
3X-RAY DIFFRACTION3{ O|* }O1 - 221
4X-RAY DIFFRACTION4{ B|* }B1 - 210
5X-RAY DIFFRACTION5{ P|* }P1 - 209
6X-RAY DIFFRACTION6{ C|* }C7 - 135
7X-RAY DIFFRACTION7{ Q|* }Q5 - 137
8X-RAY DIFFRACTION8{ D|* }D1 - 221
9X-RAY DIFFRACTION9{ R|* }R5 - 136
10X-RAY DIFFRACTION10{ E|* }E1 - 212
11X-RAY DIFFRACTION11{ F|* }F5 - 137
12X-RAY DIFFRACTION12{ G|* }G1 - 221
13X-RAY DIFFRACTION13{ H|* }H1 - 221
14X-RAY DIFFRACTION14{ I|* }I1 - 212
15X-RAY DIFFRACTION15{ J|* }J5 - 137
16X-RAY DIFFRACTION16{ K|* }K1 - 221
17X-RAY DIFFRACTION17{ L|* }L1 - 212
18X-RAY DIFFRACTION18{ M|* }M1 - 212

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