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- PDB-3v83: The 2.1 angstrom crystal structure of diferric human transferrin -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3v83
TitleThe 2.1 angstrom crystal structure of diferric human transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / iron binding domain / iron carrier/transporter / transferrin receptor / serum
Function / homology
Function and homology information


iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / iron ion transport / Iron uptake and transport / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / regulation of protein stability / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / antibacterial humoral response / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / transmembrane transporter binding / intracellular iron ion homeostasis / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / enzyme binding / 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 / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin ...Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / : / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsNoinaj, N. / Steere, A. / Mason, A.B. / Buchanan, S.K.
CitationJournal: Nature / Year: 2012
Title: Structural basis for iron piracy by pathogenic Neisseria.
Authors: Noinaj, N. / Easley, N.C. / Oke, M. / Mizuno, N. / Gumbart, J. / Boura, E. / Steere, A.N. / Zak, O. / Aisen, P. / Tajkhorshid, E. / Evans, R.W. / Gorringe, A.R. / Mason, A.B. / Steven, A.C. / Buchanan, S.K.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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: Serotransferrin
B: Serotransferrin
C: Serotransferrin
D: Serotransferrin
E: Serotransferrin
F: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,50588
Polymers462,9236
Non-polymers9,58282
Water42,0292333
1
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,71513
Polymers77,1541
Non-polymers1,56112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,81716
Polymers77,1541
Non-polymers1,66315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,90715
Polymers77,1541
Non-polymers1,75314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,81716
Polymers77,1541
Non-polymers1,66315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,81716
Polymers77,1541
Non-polymers1,66315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,43312
Polymers77,1541
Non-polymers1,27911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)254.531, 173.004, 150.151
Angle α, β, γ (deg.)90.00, 123.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-706-

SO4

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 77153.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02787

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Non-polymers , 5 types, 2415 molecules

#2: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CHO3
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2333 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, pH 7.5, 1.6 M ammonium sulfate, and 2% PEG 1000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 297056 / Num. obs: 297056 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.46 / % possible all: 91.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.102→29.947 Å / SU ML: 0.27 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 --random
Rwork0.18 ---
obs-297056 94.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.368 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8422 Å2-0 Å2-3.925 Å2
2--3.2319 Å2-0 Å2
3----1.3898 Å2
Refinement stepCycle: LAST / Resolution: 2.102→29.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31049 0 546 2333 33928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832343
X-RAY DIFFRACTIONf_angle_d1.14543511
X-RAY DIFFRACTIONf_dihedral_angle_d15.35611781
X-RAY DIFFRACTIONf_chiral_restr0.0854628
X-RAY DIFFRACTIONf_plane_restr0.0055632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1015-2.12540.30374600.26778667X-RAY DIFFRACTION87
2.1254-2.15040.30264580.26129066X-RAY DIFFRACTION91
2.1504-2.17660.31345150.25339173X-RAY DIFFRACTION92
2.1766-2.20420.29294770.24529072X-RAY DIFFRACTION92
2.2042-2.23320.28784900.23519105X-RAY DIFFRACTION92
2.2332-2.26380.29715150.23639131X-RAY DIFFRACTION92
2.2638-2.29610.30044680.22649194X-RAY DIFFRACTION92
2.2961-2.33030.2694740.21539143X-RAY DIFFRACTION92
2.3303-2.36670.26875070.21319171X-RAY DIFFRACTION92
2.3667-2.40550.28755020.21929205X-RAY DIFFRACTION93
2.4055-2.4470.27154960.2129278X-RAY DIFFRACTION93
2.447-2.49150.2514990.20159231X-RAY DIFFRACTION93
2.4915-2.53940.24124760.19669281X-RAY DIFFRACTION93
2.5394-2.59120.2454660.20439291X-RAY DIFFRACTION94
2.5912-2.64750.26794910.20289429X-RAY DIFFRACTION94
2.6475-2.7090.26244950.19029406X-RAY DIFFRACTION95
2.709-2.77670.23894810.19179418X-RAY DIFFRACTION95
2.7767-2.85170.25775030.19369552X-RAY DIFFRACTION96
2.8517-2.93560.25795240.20219530X-RAY DIFFRACTION96
2.9356-3.03020.23465160.18679626X-RAY DIFFRACTION97
3.0302-3.13840.22015080.18299744X-RAY DIFFRACTION97
3.1384-3.2640.2295350.18439692X-RAY DIFFRACTION97
3.264-3.41230.21375000.17299669X-RAY DIFFRACTION97
3.4123-3.59190.19994940.16359737X-RAY DIFFRACTION97
3.5919-3.81660.1975160.15479674X-RAY DIFFRACTION97
3.8166-4.11060.1925330.14639694X-RAY DIFFRACTION97
4.1106-4.52290.17245570.13979711X-RAY DIFFRACTION97
4.5229-5.17450.18365550.14769710X-RAY DIFFRACTION97
5.1745-6.50830.21294980.17869753X-RAY DIFFRACTION97
6.5083-29.94990.18265170.17369717X-RAY DIFFRACTION96
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)
12.6118-0.194-0.70941.64440.06541.6687-0.0309-0.1844-0.2123-0.0062-0.0464-0.01580.07160.09640.06930.13960.01210.0450.160.04980.1542-57.198636.3542-20.6969
21.83091.19711.21055.52962.38382.9975-0.10670.1501-0.0202-0.4185-0.0440.34960.0177-0.31120.23940.31180.02640.0980.322-0.00570.2927-60.64349.0125-46.4431
31.8941-0.833-0.5342.73030.47351.9943-0.3942-0.1351-0.51420.1630.1181-0.23980.46810.17820.2360.38370.11940.2530.29330.06060.5406-46.7469-2.4608-38.1638
41.3773-0.04150.43830.74-0.01810.9467-0.00710.03540.1045-0.0873-0.0067-0.0554-0.05570.05730.0330.1482-0.00910.07950.1677-0.01040.147412.2643-14.6125-20.298
52.8691.083-0.42634.181-2.02842.874-0.10930.4304-0.0525-0.7422-0.0025-0.25930.21010.30050.15020.3757-0.02090.04490.3611-0.00580.260713.039812.8236-46.8038
62.4264-1.04370.63933.0569-0.34292.7702-0.3361-0.17610.3691-0.00530.08080.378-0.5427-0.49110.16640.26380.0847-0.09480.2685-0.03560.3786-3.119324.8309-37.5851
74.5323-0.37610.03914.20460.51112.8962-0.2495-0.00040.45490.00780.1715-0.1294-0.44660.1320.12750.25640.055-0.12440.2250.01440.260211.140220.7412-35.0378
80.6877-0.1380.07571.42920.12722.80630.0140.0148-0.0668-0.0791-0.0156-0.10590.12310.0745-0.00080.10240.01590.05080.10060.00240.187-34.550336.8862-67.3963
92.60772.91021.1273.42451.15760.36210.5029-0.5758-0.11850.5657-0.6940.17590.2865-0.6582-0.03960.4145-0.16250.03330.4438-0.02830.3952-57.064513.9014-72.86
101.2339-0.01730.73562.37220.95850.99780.78690.2879-1.4023-0.22060.1582-2.2405-0.01460.1724-0.39520.4335-0.18210.0092-0.025-0.53221.8391-44.0785-4.3421-88.6749
110.8762-0.67970.17583.46340.9082.14880.5273-0.4172-0.88530.7956-0.2098-0.95230.6762-0.2066-0.28350.6591-0.1882-0.25330.4710.08680.847-49.48480.4671-74.4867
121.79580.451-0.57131.4573-0.19540.86970.08090.12810.11680.0337-0.03750.0037-0.1026-0.0742-0.02510.15590.04180.04620.20370.04720.1448-62.6829-14.400217.2801
132.08230.41370.10482.2331-0.81522.6196-0.01380.1490.4413-0.0776-0.1478-0.0472-0.19110.18360.12230.14820.02050.02640.23110.11390.3497-42.243722.712517.4107
142.1069-0.13641.02791.1340.05991.42190.085-0.0941-0.13340.0053-0.0232-0.03880.1222-0.0082-0.04660.1512-0.010.06680.1460.03040.1291-108.253436.0527-15.8051
152.5269-0.41-1.08254.04351.38123.28490.02880.4642-0.0352-0.4329-0.0006-0.3219-0.0370.21150.08910.24170.0530.06240.33980.06120.3271-88.02749.3089-32.6209
162.438-0.8713-0.29341.9238-0.97882.0531-0.2231-0.2922-0.56020.082-0.1582-0.1220.42230.64490.26090.31570.16260.10720.43670.20750.391-85.1879-3.8274-16.3526
172.06940.018-0.12433.19890.42.9809-0.105-0.3947-0.37620.36650.03940.56590.393-0.09270.09450.25620.04380.06280.29660.11340.3564-97.07272.8618-16.0838
180.9022-0.04530.17441.4389-0.1362.99550.01850.03130.0712-0.04490.02210.0452-0.2156-0.0231-0.0010.13370.0210.06770.11370.02020.1683-9.0676-15.4629-66.3398
193.36391.6608-0.90733.1689-0.19621.610.2703-0.3371-0.01530.1024-0.2134-0.3473-0.18350.349-0.01170.2934-0.02830.11460.25540.0340.265410.852411.9952-75.0077
201.9922-0.7786-0.18351.7941-0.59291.53440.44240.28110.5382-0.0628-0.1595-0.0989-0.1730.0256-0.18450.35790.05880.25970.29040.0610.4791.379426.9011-86.3477
212.2668-0.33640.13292.72920.27182.20970.3268-0.25010.63470.294-0.12870.0761-0.55740.0561-0.1640.46090.0030.24530.2652-0.02890.36733.703520.0474-74.9355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 23:335)
2X-RAY DIFFRACTION2chain 'A' and (resseq 336:380)
3X-RAY DIFFRACTION3chain 'A' and (resseq 381:677)
4X-RAY DIFFRACTION4chain 'B' and (resseq 20:347)
5X-RAY DIFFRACTION5chain 'B' and (resseq 348:380)
6X-RAY DIFFRACTION6chain 'B' and (resseq 381:595)
7X-RAY DIFFRACTION7chain 'B' and (resseq 596:677)
8X-RAY DIFFRACTION8chain 'C' and (resseq 23:317)
9X-RAY DIFFRACTION9chain 'C' and (resseq 318:380)
10X-RAY DIFFRACTION10chain 'C' and (resseq 381:592)
11X-RAY DIFFRACTION11chain 'C' and (resseq 593:677)
12X-RAY DIFFRACTION12chain 'D' and (resseq 22:347)
13X-RAY DIFFRACTION13chain 'D' and (resseq 348:677)
14X-RAY DIFFRACTION14chain 'E' and (resseq 23:335)
15X-RAY DIFFRACTION15chain 'E' and (resseq 336:380)
16X-RAY DIFFRACTION16chain 'E' and (resseq 381:627)
17X-RAY DIFFRACTION17chain 'E' and (resseq 628:677)
18X-RAY DIFFRACTION18chain 'F' and (resseq 21:335)
19X-RAY DIFFRACTION19chain 'F' and (resseq 336:411)
20X-RAY DIFFRACTION20chain 'F' and (resseq 412:609)
21X-RAY DIFFRACTION21chain 'F' and (resseq 610:677)

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