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- PDB-7q1l: Glycosilated Human Serum Apo-tranferrin -

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Basic information

Entry
Database: PDB / ID: 7q1l
TitleGlycosilated Human Serum Apo-tranferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Serotransferrin / iron-free (Apo)
Function / homology
Function and homology information


iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGavira, J.A. / Moreno, A. / Campos-Escamilla, C. / Gonzalez-Ramirez, L.A. / Siliqi, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116261GB-I00 Spain
CitationJournal: Int J Mol Sci / Year: 2021
Title: X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin.
Authors: Campos-Escamilla, C. / Siliqi, D. / Gonzalez-Ramirez, L.A. / Lopez-Sanchez, C. / Gavira, J.A. / Moreno, A.
History
DepositionOct 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serotransferrin
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,80816
Polymers149,9742
Non-polymers1,83414
Water1267
1
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9589
Polymers74,9871
Non-polymers9718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8507
Polymers74,9871
Non-polymers8636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.631, 102.148, 199.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 74987.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02787
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 19 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.99 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Ammonium Citrate pH 7.0, 20% PEG 3350 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 3→37.35 Å / Num. obs: 36713 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.038 / Rrim(I) all: 0.104 / Net I/σ(I): 9.9 / Num. measured all: 267933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.1381.6063535644370.590.6061.7181.3100
10.39-37.356.60.0464679790.9990.0160.04331.298

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Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
XDSdata reduction
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAV

2hav


Resolution: 3→37.35 Å / SU ML: 0.4375 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 1829 4.99 %
Rwork0.2195 34822 -
obs0.221 36651 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.52 Å2
Refinement stepCycle: LAST / Resolution: 3→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10488 0 117 7 10612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004710946
X-RAY DIFFRACTIONf_angle_d0.852514790
X-RAY DIFFRACTIONf_chiral_restr0.04481579
X-RAY DIFFRACTIONf_plane_restr0.00561933
X-RAY DIFFRACTIONf_dihedral_angle_d8.22611520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.39861330.37022636X-RAY DIFFRACTION99.89
3.08-3.170.39341300.34932650X-RAY DIFFRACTION100
3.17-3.270.34871370.332644X-RAY DIFFRACTION100
3.27-3.390.30141400.29652645X-RAY DIFFRACTION99.96
3.39-3.530.32431410.27272653X-RAY DIFFRACTION99.89
3.53-3.690.281200.25022654X-RAY DIFFRACTION99.96
3.69-3.880.29561300.23552665X-RAY DIFFRACTION99.89
3.88-4.120.22741340.21052661X-RAY DIFFRACTION99.75
4.12-4.440.20281400.18382682X-RAY DIFFRACTION99.65
4.44-4.890.21081590.16992661X-RAY DIFFRACTION100
4.89-5.590.23811530.19072695X-RAY DIFFRACTION99.96
5.59-7.040.25171700.21842709X-RAY DIFFRACTION99.86
7.04-37.350.23061420.20662867X-RAY DIFFRACTION99.73
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)
14.429565415490.0257854203221-1.372452499432.761499490030.8573867620923.61551651040.0556483501755-0.352120737222-0.621362711305-0.195055819280.005464061792170.1927858025540.0308993135533-0.560337398365-0.0885850828730.71774951529-0.00174770716934-0.1550643906310.6601654105490.1623271387860.737033811524-25.0964064883-5.3628690653713.974408588
22.27451747684-0.4691334339020.04763308844262.65541202401-0.1636628530392.65889682560.14212236060.406191011274-1.62902203124-0.572072190056-0.135720037212-0.3547381205250.4113891628190.3033269056180.1309965196921.173948932010.0814346674373-0.228712794210.5758793108-0.1293569750531.46904530272-16.9670802002-17.54109033711.29236057863
31.611477373270.4490429471760.5602659713990.528612924459-0.8347355044671.911051060330.0392812218767-0.3507604844920.1797814433850.296861044040.01946007452450.322452920081-0.0389868094484-0.06363698460.03555536028361.221450469250.00841960129618-0.02396811660550.745806961951-0.04213579859850.911976080705-34.390636881913.2928375867-4.94038435057
43.38891602560.3398266055841.146087597076.33731736587-0.005479818984873.161234972710.07798668415890.359456010836-0.0953433178715-0.7683482929050.1410723589480.5840662827120.620055657829-0.761868066334-0.1426195783910.898992221281-0.173195478739-0.02988314870610.9646534254140.04673089014390.697793014213-51.815862642-3.76148471765-23.9748966156
53.809800096911.424246351370.3216005239973.63068183678-1.21618101693.69086556960.6837603611680.5219439190220.3010716530610.909322650795-0.2667782052310.1996912352051.79504373585-0.744743090829-0.4273185798761.17518860587-0.146784016095-0.08502671321140.843914205294-0.06345493433560.550075822744-42.6602637096-7.36034895624-8.83596959499
64.08220173034-0.840861125138-0.01220169569681.953119544810.7400251714972.559378012150.2483298998270.0621409190192-1.19232864705-0.225076865407-0.15360967271-0.3283853886870.211380036475-0.0193492346655-0.1328386512920.621798297648-0.0262681507106-0.02593552015030.5168923945470.009014515951071.010514100147.38173747228-4.5081053997918.4735234495
74.619760721871.139485846070.2184174500793.013448871041.11722651612.644539044530.299847628042-0.824156867798-0.8416902857020.16198452745-0.165037660881-0.1546426695410.1116018353320.427498300899-0.172733351590.788308187007-0.0393712735376-0.1219319470360.8738817304240.2287639716360.9647520305625.182653056650.87236216939631.9072276553
83.016114240321.83189939116-0.4077862296313.2036309681-1.288702290980.706344172734-0.1792642683820.7401306828-0.590777203093-1.22382975811-0.0931468829135-0.61704195669-0.131158804483-0.1350855663540.2017839715580.9192125461780.07963057935870.1040748492220.845770311146-0.02333016548340.78556492151819.01345934521.921194442614.6408546747
91.97447700735-1.163379221631.447688506672.77126205653-0.03483756108432.91900429692-0.0296139926538-1.05454871952-0.06450965468340.649598621005-0.138764095373-0.6375079158740.3901744958630.9604827297720.1549486252790.799342103522-0.108569843144-0.1211111068791.412520349560.1165985430981.0593077621432.130895713223.91830777744.4011746176
103.8517976511.413377449351.481031616342.807745348421.266548100825.486000798050.160126873565-0.4234986865720.2080130496890.1704503474210.0867271244458-0.7305431954-0.2888325420740.944020019591-0.2432654040920.7422146021950.04153360924120.1360097157840.991305289477-0.09042776187140.98499541666133.770555221828.432272764236.9042838148
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 259 )AA4 - 2591 - 256
22chain 'A' and (resid 260 through 316 )AA260 - 316257 - 313
33chain 'A' and (resid 317 through 392 )AA317 - 392314 - 389
44chain 'A' and (resid 393 through 640 )AA393 - 640390 - 637
55chain 'A' and (resid 641 through 679 )AA641 - 679638 - 676
66chain 'B' and (resid 4 through 226 )BH4 - 2261 - 223
77chain 'B' and (resid 227 through 316 )BH227 - 316224 - 313
88chain 'B' and (resid 317 through 392 )BH317 - 392314 - 389
99chain 'B' and (resid 393 through 489 )BH393 - 489390 - 486
1010chain 'B' and (resid 490 through 679 )BH490 - 679487 - 676

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