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- PDB-1suv: Structure of Human Transferrin Receptor-Transferrin Complex -

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Basic information

Entry
Database: PDB / ID: 1suv
TitleStructure of Human Transferrin Receptor-Transferrin Complex
DescriptorTransferrin receptor protein 1, Serotransferrin
KeywordsMETAL TRANSPORT / Protein Complex
Specimen sourceHomo sapiens / human
MethodElectron microscopy (7.5 Å resolution / Particle / Single particle)
AuthorsCheng, Y. / Zak, O. / Aisen, P. / Harrison, S.C. / Walz, T.
CitationCell, 2004, 116, 565-576

Cell, 2004, 116, 565-576 StrPapers
Structure of the human transferrin receptor-transferrin complex.
Yifan Cheng / Olga Zak / Philip Aisen / Stephen C Harrison / Thomas Walz

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 26, 2004 / Release: Apr 13, 2004
RevisionDateData content typeGroupProviderType
1.0Apr 13, 2004Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE NOT ALL THE CHAINS IN THE MODEL ARE HUMAN, ALTHOUGH THE PROTEINS USED TO DETERMINE THE 7.5 A STRUCTURE OF THE TFR-TF COMPLEX WERE ALL HUMAN. THE AUTHORS CREATED THE MODEL BY FITTING X-RAY CRYSTAL STRUCTURES INTO THEIR 7.5 A EM DENSITY MAP. SINCE THERE IS NO STRUCTURE FOR THE HUMAN TRANSFERRIN C-LOBE, THE AUTHORS OPTED TO USE THE C-LOBE FROM RABBIT TF (1JNF). THE OTHER TWO CHAINS ARE HUMAN (1CX8 - HUMAN TFR AND 1A8E - HUMAN TF N-LOBE). THE CHAINS E AND F MATCH SWS P19134, A RABBIT SOURCE. REGARDING THE CONFLICTS: BOTH SEQUENCE AND COORDINATES ARE FROM THE ORIGINAL PDB-FILES AND THE AUTHORS DID NOT MAKE ANY MODIFICATIONS TO IT.

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Assembly

Deposited unit
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1
C: Serotransferrin, N-lobe
D: Serotransferrin, N-lobe
E: Serotransferrin, C-lobe
F: Serotransferrin, C-lobe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,12714
Polyers292,6646
Non-polymers4638
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)Transferrin receptor protein 1 / TfR1 / TR / TfR / Trfr / CD71 antigen / T9 / p90


Mass: 71622.961 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P02786

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Serotransferrin, N-lobe / Transferrin / Siderophilin / Beta-1-metal binding globulin / PRO1400


Mass: 36408.414 Da / Num. of mol.: 2 / Fragment: repeat 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P02787

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)Serotransferrin, C-lobe / Transferrin / Siderophilin / Beta-1-metal binding globulin


Mass: 38300.445 Da / Num. of mol.: 2 / Fragment: repeat 2 / Source: (gene. exp.) Homo sapiens / human
#4: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Formula: CO3
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Formula: Fe

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Human Transferrin Receptor - Transferrin Complex / Type: COMPLEX
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Oct 15, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 51160 / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm / Cs: 2 mm
Specimen holderTemperature: 93 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: CTF correction for each particle
SymmetryPoint symmetry: C2
3D reconstructionMethod: Fourier Space reconstruction / Resolution: 7.5 Å / Nominal pixel size: 2.8 / Actual pixel size: 2.74 / Details: using program FREALIGN / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL
Target criteria: visual fit using program O followed by rigid body refinement using program MAVE
Atomic model building
IDPDB-ID 3D fitting ID
11CX81
21A8E1
31JNF1
Number of atoms included #LASTProtein: 20584 / Nucleic acid: 0 / Ligand: 28 / Solvent: 0 / Total: 20612

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